Kinetic exclusion amplification of nucleic acid libraries

ABSTRACT

An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser. No. 62/442,680, filed Jan. 5, 2017, and claims priority to Great Britain (GB) Patent Application Number 1704754.9, filed Mar. 24, 2017, which itself claims priority to U.S. Provisional Application Ser. No. 62/442,680, filed Jan. 5, 2017, the contents of each of which is incorporated by reference herein in its entirety.

BACKGROUND

Genetic analysis is taking on increasing importance in modern society. Genetic analyses have already proven useful for predicting a person's risk of contracting some diseases (diagnostics), determining the probability of therapeutic benefit versus the risk of side effects for a person considering certain treatments (prognostics) and identifying missing persons, perpetrators of crimes, victims of crimes and casualties of war (forensics), to name a few. However, in many cases, appropriate genetic tests are not yet available or suffer from high error rates. One source for these problems is that many of the genetic tests currently used for diagnostics, prognostics and forensics rely on technologies that probe only a fraction of a person's genome. A person's genetic traits are encoded by a genome that contains over 3 billion base pairs, and yet most genetic tests investigate mutations at only a few of these base pairs. By increasing the fraction of the genome probed, ideally up to and including all 3 billion base pairs in the genome, the accuracy of genetic tests can be improved and genetic tests can be developed for more diagnostic and prognostic situations.

A component of many genetic tests is the preparation of the genetic material that is to be tested. This is not a trivial matter when attempting to capture an entire genome and maintain its integrity. Two methods that are currently available for capturing large amounts of genetic material are emulsion polymerase chain reaction (ePCR) and cluster amplification (e.g., via bridge amplification). The use of these methods in clinical and diagnostic applications is currently limited.

For ePCR, aqueous droplets are formed in an oil phase along with genome fragments and carrier beads. Conditions are chosen to optimize the probability that each droplet will isolate an individual genome fragment and a single carrier bead. The goal is for the droplets to form micro-reactors that prevent diffusion of genome fragments between droplets and hence between different beads. Several cycles of PCR amplification can then be carried out for the bulk emulsion such that in each droplet the bead is coated with clonal copies of the extant genome fragment. After amplification the beads are transferred to a detection substrate for evaluation in an analytical instrument. One complication with ePCR is that some of the beads end up in droplets without a genome fragment, thus producing blank beads. A bead enrichment process can be carried out to remove blank beads prior to use in the analytical instrument; however, this process may be cumbersome and inefficient. Another complication with ePCR is that some droplets end up with more than one genome fragment, thus producing mixed-clone beads. Although mixed clone beads can often be identified and then ignored during analysis, their presence decreases the efficiency, and in some cases the accuracy, of the analysis.

Cluster amplification provides a more streamlined approach to the capture and amplification of genetic material. In commercial examples, genome fragments are captured on a substrate surface to form “seeds” at random locations. After washing away excess genome fragments (i.e., those that have not been captured), several cycles of amplification are carried out to create clonal copies that form a cluster on the surface around each seed. Advantages of cluster amplification compared to ePCR include avoidance of the bead enrichment step, avoidance of the bead transfer step (from the emulsion to the detection substrate), and avoidance of messy, and often finicky, oil emulsions. However, a potential complication of commercial cluster amplification techniques is that they form a random pattern of clusters on the surface. Although image registration protocols have been developed to locate and distinguish randomly located clusters, such protocols place an extra analysis burden on analytical devices. Furthermore, randomly located clusters tend to fill a surface less efficiently than is theoretically possible for a spatially ordered pattern of clusters.

Thus, there exists a need for improved methods to prepare genetic material for diagnostic, prognostic and forensic analyses. The present disclosure addresses this need and provides other advantages as well.

INTRODUCTION

In an example, a method (e.g., for amplifying nucleic acid libraries) is provided that includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over an array of amplification sites on the flow cell and subsequently flowing the second solution over the array of amplification sites. The first solution includes a number of target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates (NTPs) and one or more replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from the corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons in the clonal populations at the amplification sites.

In an example of this method, the second reagent mixture includes the NTPs and the one or more replication enzymes of the first reagent mixture.

In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein the first solution reacts on the flow cell to bind the target nucleic acids and the amplicons to a first subset of the primers, and wherein the second solution reacts on the flow cell to produce additional amplicons and bind the additional amplicons to at least some of the primers in an exposed subset of the primers different than the first subset.

This method may further include removing the first solution from the flow cell prior to flowing the second solution over the array of amplification sites on the flow cell such that the only target nucleic acids on the flow cell as the second solution flows over the array of amplification sites are bound to the flow cell and not free-floating within the first solution.

In an example of this method, the array of amplification sites are disposed along a surface of the flow cell, wherein the first solution is flowed through an inlet port of the flow cell across the surface of the flow cell, and wherein the second solution is subsequently flowed through the inlet port across the surface of the flow cell.

In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein at least some of the primers bind to the target nucleic acids in the first solution responsive to flowing the first solution over the array of amplification sites, and wherein subsequently flowing the second solution that lacks the target nucleic acids over the array of amplification sites results in no additional binding of the primers to the target nucleic acids.

In an example, the target nucleic acids are only flowed over the array of amplification sites on the flow cell with the first solution. In another example of this method, the first solution and the second solution are isothermally flowed over the array of amplification sites.

In some examples, the second reagent mixture includes the NTPs and a polymerase, and in other examples, the second reagent mixture includes one or more of a helicase and a recombinase, and in still other examples, the second reagent mixture includes a primer having at least one of a P5 primer sequence or a P7 primer sequence.

In an example of this method, the amplification sites are wells along a surface of the flow cell, the wells separated from each other by interstitial regions along the surface.

An example of this method further comprises controlling the transport rate of the target nucleic acids to the amplification sites using one or more of: controlling a concentration of the target nucleic acids in the first solution, controlling a viscosity of the first solution, controlling an average size of the target nucleic acids, and controlling a presence or absence of a molecular crowding reagent in the first solution.

Another example of this method further comprises controlling the amplification rate of the target nucleic acids using one or more of: controlling a concentration of the NTPs in the first reagent mixture, controlling a concentration of the one or more replication enzymes in the first reagent mixture, and controlling the temperature at the amplification sites.

It is to be understood that any features of the method may be combined together in any desirable manner and/or configuration.

In another example, a fluidic system (e.g., for amplifying nucleic acid libraries) is provided that includes a reagent manifold and a controller. The reagent manifold includes at least one valve in fluid communication with an inlet port of a flow cell that includes an array of amplification sites. The reagent manifold further includes a plurality of channels fluidly connected between the at least one valve and corresponding reagent reservoirs. The controller includes one or more processors. The controller is to control the at least one valve and a pump to flow a first solution through the inlet port over the array of amplification sites on the flow cell and to subsequently flow a different, second solution through the inlet port over the array of amplification sites on the flow cell. The first solution includes a number of target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates (NTPs) and one or more replication enzymes. The number of target nucleic acids in the first solution exceeds a number of the amplification sites in the array. The first solution reacts on the flow cell to produce clonal populations of amplicons at the amplification sites originating from corresponding target nucleic acids. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce the amplicons at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution reacts on the flow cell to increase a number of amplicons in the clonal populations of amplicons at the amplification sites.

In an example of this fluidic system, second reagent mixture has the same composition as the first reagent mixture.

In an example of this fluidic system, the controller is to control the at least one valve and the pump to mix a sample template that includes the target nucleic acids with the first reagent mixture to form the first solution, and wherein the controller is to control the at least one valve and the pump to form the second solution by mixing the second reagent mixture together without mixing the sample template with the second reagent mixture. In another example of this fluidic system, the controller is to control the at least one valve and the pump to remove the first solution from the flow cell prior to flowing the second solution over the array of amplification sites on the flow cell such that the only target nucleic acids that are present as the second solution flows over the array of amplification sites are bound to the flow cell and not free-floating within the first solution.

It is to be understood that any features of the fluidic system may be combined together in any desirable manner. Moreover, it is to be understood that any combination of features of the fluidic system and/or of the method may be used together, and/or that any features from either or both of these aspects may be combined with any of the examples disclosed herein.

In another example, a method (e.g., for amplifying nucleic acid libraries) is provided that includes mixing a first reagent mixture with an amount of target nucleic acids within a reservoir to define a first solution. The first reagent mixture comprises nucleoside triphosphates (NTPs) and one or more replication enzymes. The method also includes flowing the first solution from the reservoir over an array of amplification sites on a flow cell. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from the corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. Subsequent to flowing the first solution from the reservoir, the method includes mixing a second reagent mixture within the reservoir without adding an additional amount of the target nucleic acids to the reservoir to define a second solution. The second reagent mixture comprises fresh quantities of the NTPs and the one or more replication enzymes. The method further includes flowing the second solution from the reservoir over the array of amplification sites on the flow cell. The second reagent mixture reacts with the amplicons to increase a number of the amplicons in the clonal populations at the amplification sites.

In an example of this method, the first reagent mixture and the second reagent mixture both include a buffer component, the second reagent mixture including a greater quantity of the buffer component relative to the first reagent mixture to compensate for the lack of adding the additional amount of the target nucleic acids within the second solution.

It is to be understood that any features of this example of the method may be combined together in any desirable manner. Moreover, it is to be understood that any combination of features from this method and/or the fluidic system and/or the other method may be used together, and/or that any features from any or all of these aspects may be combined with any of the features of the examples disclosed herein.

BRIEF DESCRIPTIONS OF THE DRAWINGS

Features of examples of the present disclosure will become apparent by reference to the following detailed description and drawings, in which like reference numerals correspond to similar, though perhaps not identical, components. For the sake of brevity, reference numerals or features having a previously described function may or may not be described in connection with other drawings in which they appear.

FIG. 1A shows a composite image (four color channels) obtained after a first sequencing cycle for an example patterned flow cell produced by kinetic exclusion.

FIG. 1B shows a composite image (four color channels) obtained after a single sequencing cycle for an example flow cell having randomly located clusters.

FIG. 2 shows pair distribution function (PDF) and nearest neighbor (NN) functions for a composite image obtained after a first sequencing cycle using an example patterned flow cell produced by kinetic exclusion.

FIG. 3 shows, in one example, a scatter plot of spatial positions of clusters that align to the first 5 genomic positions of PhiX genome. The different genomic positions are indicated by exes, asterisks, squares, triangles and diamonds.

FIG. 4 shows, in (a) and (b), schematic and partially cross-sectional views of example flow cell architectures for electrochemical desorption of species from the flow cell surface and also shows, in (c), total internal reflection fluorescence (TIRF) microscopy images of electrode surfaces from the flow cell configuration shown in (b) after it is used for field assisted pull down of deoxyribonucleic acid (DNA). Electric potential can be applied across one conductive surface and the electrolyte as seen in (a) or across two conductive surfaces as shown in (b). The flow cell configuration shown in (b) can also be used for field assisted pull down of DNA in real time achieving over a 100× concentration of DNA on the electrode surface in a few seconds as shown in (c).

FIG. 5 shows an example workflow for electric field assisted formation of biomolecule patterns, and schematic and partially cross-sectional views of the example workflow before and after electric field application.

FIG. 6 shows, in one example, seeding of templates and cluster amplification of the templates on 2 μm gold (Au) features on an indium tin oxide (ITO) background in the presence of an electric field (a), and with no electric field (b). Corresponding line profiles show fluorescence intensity across the labeled regions.

FIG. 7 shows, in one example, large area fluorescence images following seeding and clustering in the presence of an electric field. (a) shows a flow cell lane containing 2 μm Au dots; and (b) shows a lane containing 200 nm Au dots. Clusters are aligned over large areas to the micro and nanopatterned features, the spatially ordered nature of these clusters is confirmed by the corresponding Fourier Transforms (FFTs).

FIG. 8 shows example DNA cluster formation on 700 nm diameter SiO₂ sites in the presence of electric field. Clusters are highly ordered with little fluorescence from interstitial areas.

FIG. 9 shows, in one example, (a) results of a hybridization assay in a HISEQ® instrument flow cell (1) before electric field assisted P5 and P7 primer grafting, (2) after electric field assisted P5 and P7 primer grafting, (3) after electric field assisted P5 and P7 primer grafting and re-grafting P5 and P7 primers, and (4) after electric field assisted P5 and P7 primer grafting, silane-free acrylamide (SFA) recoating and re-grafting P5 and P7 primers; and (b) a graph depicting the median fluorescence intensity (in arbitrary units, a.u.) per flow cell lane following each step.

FIG. 10 shows, in one example, (a) a schematic representation of direct hybridization on dielectric sites using electric field; (b) spatially patterned clusters formed in the presence of a nucleic acid-repellant electric field at the interstitial regions and (c) randomly ordered clusters formed in the absence of the nucleic acid-repellant electric field at the interstitial regions.

FIG. 11 is a flow chart of a method for generating genetic clusters according to an example disclosed herein.

FIG. 12 is a bar graph showing, in one example, the signal intensity (in arbitrary units, a.u.) of genetic clusters on a flow cell for different cluster generation methods.

FIG. 13 is a bar graph showing, in one example, percent passing filter (% PF) values for the cluster generation methods shown in FIG. 12.

FIG. 14 is a schematic illustration of a fluidic system for generating genetic clusters according to an example disclosed herein.

DETAILED DESCRIPTION

This disclosure provides nucleic acid libraries and methods for making nucleic acid libraries. In particular examples, a nucleic acid library of the present disclosure is in the form of an array of sites.

All literature and similar material cited in this application, including, but not limited to, patents, patent applications, articles, books, treatises, and web pages, regardless of the format of such literature and similar materials, are expressly incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs from or contradicts this application, including but not limited to defined terms, term usage, described techniques, or the like, this application controls.

The array can have sites that are clonal with respect to particular nucleotide sequences. Accordingly, individual sites in the array can each have multiple copies of a single nucleotide sequence. For example, the sites can have clonal copies of a nucleic acid derived from a biological sample, such as a genome or sub-fraction thereof (e.g., an exome), or a transcriptome (e.g., mRNA library or cDNA library) or sub-fraction thereof.

The fraction of sites in an array that are clonal can exceed the fraction predicted by the Poisson distribution. Thus, an array produced by the methods set forth herein can have a super-Poisson distribution of clonal sites. The super-Poisson distribution can result during synthesis of the array and without the need for subsequent site enrichment or site purification steps (although enrichment and purification steps can be carried out if desired in at least some examples).

In some examples, the sites can be present as features on (or in) a substrate. In such examples, the features can be clonal, the fraction of features in an array that are clonal can exceed the Poisson distribution, and the features can be spatially arranged in a repeating pattern. Thus, the sites can be spatially ordered, for example, in a rectilinear grid, hexagonal grid or other desired pattern.

A nucleic acid library of the present disclosure can be made using a method that exploits kinetic exclusion. Kinetic exclusion can occur when a process occurs at a sufficiently rapid rate to effectively exclude another event or process from occurring. Take for example, the making of a nucleic acid array where sites of the array are randomly seeded with target nucleic acids from a solution and copies of the target nucleic acid are generated in an amplification process to fill each of the seeded sites to capacity. In accordance with the kinetic exclusion methods of the present disclosure, the seeding and amplification processes can proceed simultaneously under conditions where the amplification rate exceeds the seeding rate. As such, the relatively rapid rate at which copies are made at a site that has been seeded by a first target nucleic acid will effectively exclude a second nucleic acid from seeding the site for amplification. Additional kinetic exclusion methods for amplifying nucleic acid libraries are described in US 2016/0053310 A1, which is incorporated herein by reference in its entirety.

Kinetic exclusion can exploit a relatively slow rate for making a first copy of a target nucleic acid vs. a relatively rapid rate for making subsequent copies of the target nucleic acid or of the first copy. In the example of the previous paragraph, kinetic exclusion occurs due to the relatively slow rate of target nucleic acid seeding (e.g., relatively slow diffusion or transport) vs. the relatively rapid rate at which amplification occurs to fill the site with copies of the nucleic acid seed. In another example, kinetic exclusion can occur due to a delay in the formation of a first copy of a target nucleic acid that has seeded a site (e.g., delayed or slow activation) versus the relatively rapid rate at which subsequent copies are made to fill the site. In this example, an individual site may have been seeded with several different target nucleic acids (e.g., several target nucleic acids can be present at each site prior to amplification). However, first copy formation for any given target nucleic acid can be activated randomly such that the average rate of first copy formation is relatively slow compared to the rate at which subsequent copies are generated. In this case, although an individual site may have been seeded with several different target nucleic acids, kinetic exclusion will allow only one of those target nucleic acids to be amplified. More specifically, once a first target nucleic acid has been activated for amplification, the site will rapidly fill to capacity with its copies, thereby preventing copies of a second target nucleic acid from being made at the site.

An advantage of arrays produced by methods set forth herein is that the clonal nature of the sites provides for accuracy in subsequent analysis. This avoids confounding results that would otherwise arise when detecting sites having mixed populations.

Another advantage of the arrays set forth herein is that they have a super-Poisson distribution of clonal sites. This increases the complexity of the library by avoiding loss of genetic content that could otherwise occur due to sequestration into mixed sites.

A further advantage of the methods and arrays set forth herein is the provision of an array having features on a substrate, wherein the features are spatially arranged in a repeating pattern. As set forth above, the fraction of the features that are clonal can exceed the Poisson distribution. The Poisson distribution sets a maximum of about 37% occupancy. In accordance with the methods set forth herein, the complement of features that are clonal can exceed about 40%, about 50%, about 60%, about 75% or more. Arrays produced by the methods set forth herein provide for more efficient filling of a substrate compared to random cluster arrays. Such arrays are also easier to evaluate analytically by avoiding complexities of image registration methods used for random cluster arrays.

Additionally, the methods set forth herein are advantageous for creating arrays on substrates that are patterned to facilitate detection. For example, several commercially available sequencing platforms rely on substrates having wells that provide a barrier to the diffusion of detection reagents (e.g., pyrophosphate in platforms available from 454 LifeSciences (a subsidiary of Roche, Basel Switzerland) or protons in platforms available from Ion Torrent (a subsidiary of Life Technologies, Carlsbad Calif.)) during sequence detection steps. The methods set forth herein can be advantageous for increasing the number of wells that are loaded with clonal populations as compared to standard cluster amplification methods that would be Poisson limited. The methods of the present disclosure are advantageous over ePCR methods as well by avoiding handling of emulsions and manipulations of beads.

Terms used herein will be understood to take on their ordinary meaning in the relevant art unless specified otherwise. Several terms used herein and their meanings are set forth below.

As used herein, the term “active seeding” refers to non-diffusive forces imposed on one or more nucleic acids to move the nucleic acid(s) toward or away from a location. The location can be an amplification site of an array. Non-diffusive forces can be provided by an external source, such as those that produce an electrical or magnetic fields, or an agent that imposes molecular crowding or chemical gradients within a reaction volume.

As used herein, the term “amplicon,” when used in reference to a nucleic acid, means the product of copying the nucleic acid, wherein the product has a nucleotide sequence that is the same as or complementary to at least a portion of the nucleotide sequence of the nucleic acid. An amplicon can be produced by any of a variety of amplification methods that use the nucleic acid, or an amplicon thereof, as a template including, for example, polymerase extension, polymerase chain reaction (PCR), rolling circle amplification (RCA), ligation extension, or ligation chain reaction. An amplicon can be a nucleic acid molecule having a single copy of a particular nucleotide sequence (e.g., a PCR product) or multiple copies of the nucleotide sequence (e.g., a concatameric product of RCA). A first amplicon of a target nucleic acid may be a complementary copy. Subsequent amplicons are copies that are created, after generation of the first amplicon, from the target nucleic acid or from the first amplicon. A subsequent amplicon can have a sequence that is at least substantially complementary to the target nucleic acid or at least substantially identical to the target nucleic acid.

As used herein, the term “amplification site” refers to a site in or on an array where one or more amplicons can be generated. An amplification site can be further configured to contain, hold or attach at least one amplicon that is generated at the site.

As used herein, the term “array” refers to a population of sites that can be differentiated from each other according to relative location. Different molecules that are at different sites of an array can be differentiated from each other according to the locations of the sites in the array. An individual site of an array can include one or more molecules of a particular type. For example, a site can include a single target nucleic acid molecule having a particular sequence or a site can include several nucleic acid molecules having the same sequence (and/or complementary sequence, thereof). The sites of an array can be different features located on the same substrate. Example features include without limitation, wells in a substrate, beads (or other particles) in or on a substrate, projections from a substrate, ridges on a substrate or channels in a substrate. The sites of an array can be separate substrates each bearing a different molecule. Different molecules attached to separate substrates can be identified according to the locations of the substrates on a surface to which the substrates are associated or according to the locations of the substrates in a liquid or gel. Example arrays in which separate substrates are located on a surface include, without limitation, those having beads in wells.

As used herein, the term “capacity,” when used in reference to a site and nucleic acid material, means the maximum amount of nucleic acid material that can occupy the site. For example, the term can refer to the total number of nucleic acid molecules that can occupy the site in a particular condition. Other measures can be used as well including, for example, the total mass of nucleic acid material or the total number of copies of a particular nucleotide sequence that can occupy the site in a particular condition. The capacity of a site for a target nucleic acid may be at least substantially equivalent to the capacity of the site for amplicons of the target nucleic acid.

As used herein, the term “capture agent” refers to a material, chemical, molecule or moiety thereof that is capable of attaching, retaining or binding to a target molecule (e.g., a target nucleic acid). Example capture agents include, without limitation, a capture nucleic acid that is complementary to at least a portion of a target nucleic acid, a member of a receptor-ligand binding pair (e.g., avidin, streptavidin, biotin, lectin, carbohydrate, nucleic acid binding protein, epitope, antibody, etc.) capable of binding to a target nucleic acid (or linking moiety attached thereto), or a chemical reagent capable of forming a covalent bond with a target nucleic acid (or linking moiety attached thereto).

As used herein, the term “clonal population” refers to a population of nucleic acids that is homogeneous with respect to a particular nucleotide sequence. The homogenous sequence may be at least about 10 nucleotides long, but can be even longer including for example, at least about 50, about 100, about 250, about 500 or about 1000 nucleotides long. A clonal population can be derived from a single target nucleic acid or template nucleic acid. Most, if not all, of the nucleic acids in a clonal population have the same nucleotide sequence. It will be understood that a small number of mutations (e.g., due to amplification artifacts) can occur in a clonal population without departing from clonality.

As used herein, the term “denaturation cycle” refers to a manipulation of a nucleic acid amplification reaction that changes the course of the amplification reaction such that complementary nucleic acid strands become separated from each other. Example manipulations include, for example, introducing a chemical reagent that denatures nucleic acids, or physically altering the reaction, by heating or other manipulation, to denature nucleic acids. Several denaturation cycles can be included in a cyclic amplification reaction. Several other cycles can also be included such as cyclic manipulations to induce a primer to hybridize to a nucleic acid strand. One or more denaturation cycles or other cycles can be omitted in a method set forth herein. As such, an amplification reaction of the present disclosure can be carried out without cyclical manipulations in at least some examples.

As used herein, the term “different”, when used in reference to nucleic acids, means that the nucleic acids have nucleotide sequences that are not the same as each other. Two or more nucleic acids can have nucleotide sequences that are different along their entire length. Alternatively, two or more nucleic acids can have nucleotide sequences that are different along a substantial portion of their length. For example, two or more nucleic acids can have target nucleotide sequence portions that are different from each other while also having a universal sequence region that are the same as each other.

As used herein, the term “fluidic access,” when used in reference to a molecule in a fluid and a site in contact with the fluid, refers to the ability of the molecule to move in or through the fluid to contact or enter the site. The term can also refer to the ability of the molecule to separate from or exit the site to enter the solution. Fluidic access can occur when there are no barriers that prevent the molecule from entering the site, contacting the site, separating from the site and/or exiting the site. However, fluidic access is understood to exist even if diffusion is retarded, reduced or altered, so long as access is not absolutely prevented.

As used herein, the term “double stranded,” when used in reference to a nucleic acid molecule, means that at least substantially all of the nucleotides in the nucleic acid molecule are hydrogen bonded to a complementary nucleotide. A partially double stranded nucleic acid can have at least about 10%, about 25%, about 50%, about 60%, about 70%, about 80%, about 90% or about 95% of its nucleotides hydrogen bonded to a complementary nucleotide.

As used herein, the term “each,” when used in reference to a collection of items, is intended to identify an individual item in the collection but does not necessarily refer to every item in the collection unless the context clearly dictates otherwise.

As used herein, the term “about,” when used in reference to a numerical value indicates approximately the value as stated, such as within ±5% of the value.

As used herein, the term “at least substantially,” when used in reference to modifying an adjective, indicates a degree that is either at or near the subject adjective, such as within ±5% margin. For example, the phrase “at least substantially all of the nucleic acids” can refer to all (e.g., 100%) of the nucleic acids or less than all of the nucleic acids within the designated margin, such as 95%-99.99% of the nucleic acids.

As used herein, the term “trace amount” refers to a very low concentration of an analyte in a mixture or solution, such as less than or equal to about 100 ppm.

As used herein, the term “excluded volume” refers to the volume of space occupied by a particular molecule to the exclusion of other such molecules.

As used herein, the term “extendible” or “extendible state,” when used in reference to a nucleic acid such as a primer, means that the nucleic acid is competent for addition of a nucleotide (e.g., via polymerase catalysis) or addition of an oligonucleotide (e.g., via ligase catalysis). A nucleic acid that is “non-extendible” or in a “non-extendible state” is not so competent, for example, due to the presence of an extension blocking moiety or the absence of a 3′ hydroxyl.

As used herein, the term “interstitial region” refers to an area in a substrate or on a surface that separates other areas of the substrate or surface. For example, an interstitial region can separate one feature of an array from another feature of the array. The two regions that are separated from each other can be discrete, lacking contact with each other. In another example, an interstitial region can separate a first portion of a feature from a second portion of a feature. The separation provided by an interstitial region can be partial or full separation. Interstitial regions may have a surface material that differs from the surface material of the features on the surface. For example, features of an array can have an amount or concentration of capture agents or primers that exceeds the amount or concentration present at the interstitial regions. In some examples, the capture agents or primers may not be present at the interstitial regions.

As used herein, the term “polymerase” is intended to be consistent with its use in the art and includes, for example, an enzyme that produces a complementary replicate of a nucleic acid molecule using the nucleic acid as a template strand. DNA polymerases may bind to the template strand and then move down the template strand sequentially adding nucleotides to the free hydroxyl group at the 3′ end of a growing strand of nucleic acid. DNA polymerases synthesize complementary DNA molecules from DNA templates, and ribonucleic acid (RNA) polymerases synthesize RNA molecules from DNA templates (transcription). Polymerases can use a short RNA or DNA strand, called a primer, to begin strand growth. Some polymerases can displace the strand upstream of the site where they are adding bases to a chain. Such polymerases are said to be strand displacing, meaning they have an activity that removes a complementary strand from a template strand being read by the polymerase. Example polymerases having strand displacing activity include, for example, the large fragment of Bst (Bacillus stearothermophilus) polymerase, exo-Klenow polymerase or sequencing grade T7 exo-polymerase. Some polymerases degrade the strand in front of them, effectively replacing it with the growing chain behind (5′ exonuclease activity). Some polymerases have an activity that degrades the strand behind them (3′ exonuclease activity). Some useful polymerases have been modified, either by mutation or otherwise, to reduce or eliminate 3′ and/or 5′ exonuclease activity.

As used herein, the term “nucleic acid” is intended to be consistent with its use in the art and includes naturally occurring nucleic acids or functional analogs thereof. Particularly useful functional analogs are capable of hybridizing to a nucleic acid in a sequence specific fashion or capable of being used as a template for replication of a particular nucleotide sequence. Naturally occurring nucleic acids generally have a backbone containing phosphodiester bonds. An analog structure can have an alternate backbone linkage including any of a variety of those known in the art. Naturally occurring nucleic acids generally have a deoxyribose sugar (e.g. found in deoxyribonucleic acid (DNA)) or a ribose sugar (e.g., found in ribonucleic acid (RNA)). A nucleic acid can contain any of a variety of analogs of these sugar moieties that are known in the art. A nucleic acid can include native or non-native bases. In this regard, a native deoxyribonucleic acid can have one or more bases selected from the group consisting of adenine, thymine, cytosine or guanine, and a ribonucleic acid can have one or more bases selected from the group consisting of uracil, adenine, cytosine or guanine. Useful non-native bases that can be included in a nucleic acid are known in the art. The term “target,” when used in reference to a nucleic acid, is intended as a semantic identifier for the nucleic acid in the context of a method or composition set forth herein and does not necessarily limit the structure or function of the nucleic acid beyond what is otherwise explicitly indicated.

As used herein, the term “rate,” when used in reference to transport, amplification, capture or other chemical processes, is intended to be consistent with its meaning in chemical kinetics and biochemical kinetics. Rates for two processes can be compared with respect to maximum rates (e.g., at saturation), pre-steady state rates (e.g., prior to equilibrium), kinetic rate constants, or other measures known in the art. In particular examples, a rate for a particular process can be determined with respect to the total time for completion of the process. For example, an amplification rate can be determined with respect to the time taken for amplification to be complete. However, a rate for a particular process need not be determined with respect to the total time for completion of the process.

As used herein, the term “recombinase” is intended to be consistent with its use in the art and includes, for example, RecA protein, the T4 uvsX protein, any homologous protein or protein complex from any phyla, or functional variants thereof. Eukaryotic RecA homologues are generally named Rad51 after the first member of this group to be identified. Other non-homologous recombinases may be utilized in place of RecA, for example, RecT or RecO.

As used herein, the term “single stranded binding protein” is intended to refer to any protein having a function of binding to a single stranded nucleic acid, for example, to prevent premature annealing, to protect the single-stranded nucleic acid from nuclease digestion, to remove secondary structure from the nucleic acid, or to facilitate replication of the nucleic acid. The term is intended to include, for example, proteins that are formally identified as Single Stranded Binding proteins by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Example single stranded binding proteins include, for example, E. coli SSB, T4 gp32, T7 gene 2.5 SSB, phage phi 29 SSB, any homologous protein or protein complex from any phyla, or functional variants thereof.

As used herein, the term “transport” refers to movement of a molecule through a fluid. The term can include passive transport, such as movement of molecules along their concentration gradient (e.g., passive diffusion). The term can also include active transport, whereby molecules can move along their concentration gradient or against their concentration gradient. Thus, transport can include applying energy to move one or more molecule in a desired direction or to a desired location such as an amplification site.

As used herein, the term “universal sequence” refers to a region of sequence that is common to two or more nucleic acid molecules where the molecules also have regions of sequence that differ from each other. A universal sequence that is present in different members of a collection of molecules can allow capture of multiple different nucleic acids using a population of universal capture nucleic acids that are complementary to the universal sequence. Similarly, a universal sequence present in different members of a collection of molecules can allow the replication or amplification of multiple different nucleic acids using a population of universal primers that are complementary to the universal sequence. Thus, a universal capture nucleic acid or a universal primer includes a sequence that can hybridize specifically to a universal sequence. Target nucleic acid molecules may be modified to attach universal adapters, for example, at one or both ends of the different target sequences.

The present disclosure discloses a method for amplifying nucleic acids. The method includes (a) providing an amplification reagent including (i) an array of amplification sites, and (ii) a solution having a plurality of different target nucleic acids; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each have a clonal population of amplicons from an individual target nucleic acid from the solution, wherein the reacting includes simultaneously (i) transporting the different target nucleic acids to the amplification sites at an average transport rate, and (ii) amplifying the target nucleic acids at the amplification sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. In particular examples, the number of the different target nucleic acids in the solution exceeds the number of amplification sites in the array. The different target nucleic acids have fluidic access to the plurality of amplification sites. Furthermore, each of the amplification sites can optionally have a capacity for several nucleic acids in the plurality of different nucleic acids.

Also disclosed is a method for amplifying nucleic acids that includes (a) providing an amplification reagent including (i) an array of amplification sites, and (ii) a solution having a plurality of different target nucleic acids; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each includes a clonal population of amplicons from an individual target nucleic acid from the solution, wherein the reacting includes (i) producing a first amplicon from an individual target nucleic acid at each of the amplification sites, and (ii) producing subsequent amplicons from the individual target nucleic acid at each of the amplification sites or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated at the amplification sites exceeds the average rate at which the first amplicon is generated at the amplification sites. In particular examples, the number of the different target nucleic acids in the solution exceeds the number of amplification sites in the array. The different target nucleic acids have fluidic access to the plurality of amplification sites. Furthermore, each of the amplification sites can optionally have a capacity for several nucleic acids in the plurality of different nucleic acids.

The present disclosure further discloses a method for amplifying nucleic acids that includes (a) providing an amplification reagent including (i) an array of amplification sites, and (ii) a solution having a plurality of different target nucleic acids; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each have a clonal population of amplicons from an individual target nucleic acid from the solution. The reacting includes simultaneously (i) capturing the different target nucleic acids at the amplification sites at an average capture rate, and (ii) amplifying the target nucleic acids captured at the amplification sites at an average amplification rate. The average amplification rate exceeds the average capture rate.

Also disclosed is a method for amplifying nucleic acids that includes (a) providing an amplification reagent including (i) an array of amplification sites, and (ii) a solution having a plurality of different target nucleic acids; and (b) reacting the amplification reagent to produce a plurality of amplification sites that each include a clonal population of amplicons from an individual target nucleic acid from the solution. The reacting includes (i) producing a first amplicon from an individual target nucleic acid that is captured at the amplification site(s), and (ii) producing subsequent amplicons from the individual target nucleic acid that is captured at each of the amplification sites or from the first amplicon. The average rate at which the subsequent amplicons are generated at the amplification sites exceeds the average rate at which the first amplicon is generated at the amplification sites.

Further disclosed is a method for creating a patterned surface of biomolecules that includes (a) providing a reagent including (i) an array having non-contiguous features on a surface such that the features are separated by interstitial regions of the surface, and (ii) a solution having a plurality of different target biomolecules; and (b) reacting the reagent to transport the biomolecules to the features and attach an individual biomolecule to each of the features. An electric field is applied to the interstitial regions to repel the biomolecules from the interstitial regions.

An array of amplification sites used in a method set forth herein can be present as one or more substrates. Examples of substrate materials that can be used for an array include glass (e.g., modified glass, functionalized glass, inorganic glasses), microspheres (e.g., inert and/or magnetic particles), plastics, polysaccharides, nylon, nitrocellulose, ceramics, resins, silica, silica-based materials, carbon, metals, an optical fiber or optical fiber bundles, polymers and multiwell (e.g., microtiter) plates. Example plastics include acrylics, polystyrene, copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes and polytetrafluoroethylene (e.g., TEFLON® from DuPont). Example silica-based materials include silicon and various forms of modified silicon.

In particular examples, a substrate can be within or part of a vessel such as a well, tube, channel, cuvette, Petri plate, bottle or the like. A particularly useful vessel is a flow cell, for example, as described in U.S. Patent Publ. No. 2010/0111768 A1 or Bentley et al., Nature 456:53-59 (2008), each of which is incorporated herein by reference in its entirety. Example flow cells are those that are commercially available from Illumina, Inc. (San Diego, Calif.). Another particularly useful vessel is a well in a multiwell plate or microtiter plate.

In some examples, the sites of an array can be configured as features on a surface. The features can be present in any of a variety of desired formats. For example, the sites can be wells, pits, channels, ridges, raised regions, pegs, posts or the like. As set forth above, the sites can contain beads. However, in particular examples the sites need not contain a bead or particle. Example sites include wells that are present in substrates used for commercial sequencing platforms sold by 454 LifeSciences (a subsidiary of Roche, Basel Switzerland) or Ion Torrent (a subsidiary of Life Technologies, Carlsbad Calif.). Other substrates having wells include, for example, etched fiber optics and other substrates described in U.S. Pat. Nos. 6,266,459; 6,355,431; 6,770,441; 6,859,570; 6,210,891; 6,258,568; 6,274,320; U.S. Patent Publ. No. 2009/0026082 A1; U.S. Patent Publ. No. 2009/0127589 A1; U.S. Patent Publ. No. 2010/0137143 A1; U.S. Patent Publ. No. 2010/0282617 A1 or PCT Publication No. WO 00/63437, each of which is incorporated herein by reference in its entirety. In several cases, the substrates are exemplified in these references for applications that use beads in the wells. The well-containing substrates can be used with or without beads in the methods or compositions of the present disclosure. In some examples, wells of a substrate can include gel material (with or without beads) as set forth in U.S. Pat. No. 9,512,422, which is incorporated herein by reference in its entirety.

The sites of an array can be metal features on a non-metallic surface such as glass, plastic or other materials exemplified above. A metal layer can be deposited on a surface using methods known in the art, such as wet plasma etching, dry plasma etching, atomic layer deposition, ion beam etching, chemical vapor deposition, vacuum sputtering or the like. Any of a variety of commercial instruments can be used as appropriate including, for example, the FLEXAL®, OPAL™, IONFAB® 300plus, or OPTOFAB® 3000 systems (Oxford Instruments, UK). A metal layer can also be deposited by e-beam evaporation or sputtering as set forth in Thornton, Ann. Rev. Mater. Sci. 7:239-60 (1977), which is incorporated herein by reference in its entirety. Metal layer deposition techniques, such as those exemplified above, can be combined with photolithography techniques to create metal regions or patches on a surface. Example methods for combining metal layer deposition techniques and photolithography techniques are provided in Examples I and II below and in U.S. Pat. No. 8,778,848, which is incorporated herein by reference in its entirety.

An array of features can appear as a grid of spots or patches. The features can be located in a repeating pattern or in an irregular non-repeating pattern. Particularly useful patterns are hexagonal patterns, rectilinear patterns, grid patterns, patterns having reflective symmetry, patterns having rotational symmetry, or the like. Asymmetric patterns can also be useful. The pitch can be the same between different pairs of nearest neighbor features or the pitch can vary between different pairs of nearest neighbor features. In particular examples, features of an array can each have an area that is larger than about 100 nm², about 250 nm², about 500 nm², about 1 μm², about 2.5 μm², about 5 μm², about 10 μm², about 100 μm², or about 500 μm². Alternatively or additionally, features of an array can each have an area that is smaller than about 1 mm², about 500 μm², about 100 μm², about 25 μm², about 10 μm², about 5 μm², about 1 μm², about 500 nm², or about 100 nm². Indeed, a region can have a size that is in a range between an upper and lower limit selected from those exemplified above.

For examples that include an array of features on a surface, the features can be discrete, being separated by interstitial regions. The size of the features and/or spacing between the regions can vary such that arrays can be high density, medium density or lower density. High density arrays are characterized as having regions separated by less than about 15 μm. Medium density arrays have regions separated by about 15 to about 30 μm, while low density arrays have regions separated by greater than about 30 μm. An array useful in one or more examples can have regions that are separated by less than about 100 μm, about 50 μm, about 10 μm, about 5 μm, about 1 μm or about 0.5 μm.

In particular examples, an array can include a collection of beads or other particles. The particles can be suspended in a solution or they can be located on the surface of a substrate. Examples of bead arrays in solution are those commercialized by Luminex (Austin, Tex.). Examples of arrays having beads located on a surface include those wherein beads are located in wells such as a BEADCHIP™ array (Illumina Inc., San Diego Calif.) or substrates used in sequencing platforms from 454 LifeSciences (a subsidiary of Roche, Basel Switzerland) or Ion Torrent (a subsidiary of Life Technologies, Carlsbad Calif.). Other arrays having beads located on a surface are described in U.S. Pat. Nos. 6,266,459; 6,355,431; 6,770,441; 6,859,570; 6,210,891; 6,258,568; 6,274,320; U.S. Patent Publ. No. 2009/0026082 A1; U.S. Patent Publ. No. 2009/0127589 A1; U.S. Patent Publ. No. 2010/0137143 A1; U.S. Patent Publ. No. 2010/0282617 A1 or PCT Publication No. WO 00/63437, each of which is incorporated herein by reference in its entirety. Several of the above references describe methods for attaching target nucleic acids to beads prior to loading the beads in or on an array substrate. It will however, be understood that the beads can be made to include amplification primers and the beads can then be used to load an array, thereby forming amplification sites for use in a method set forth herein. As set forth previously herein, the substrates can be used without beads. For example, amplification primers can be attached directly to the wells or to gel material in wells. Thus, the references are illustrative of materials, compositions or apparatus that can be modified for use in the methods and compositions set forth herein.

Amplification sites of an array can include a plurality of capture agents capable of binding to target nucleic acids. Example capture agents include receptors and/or ligands having a respective binding partner attached to the target nucleic acids, examples of which are set forth previously herein. A particularly useful capture agent is a capture nucleic acid that is complementary to a sequence of one or more target nucleic acids. For example, capture nucleic acids that are present at an amplification site can have a universal capture sequence that is complementary to a universal sequence that is present in an adapter sequence of each target nucleic acid. In some examples, the capture nucleic acid can also function as a primer for amplification of the target nucleic acid (whether or not it also contains a universal sequence).

In particular examples, a capture agent, such as a capture nucleic acid, can be attached to the amplification site. For example, the capture agent can be attached to the surface of a feature of an array. The attachment can be via an intermediate structure such as a bead, particle or gel. Attachment of capture nucleic acids to an array via a gel is shown in Example I below and further exemplified by flow cells available commercially from Illumina Inc. (San Diego, Calif.) or described in WO 2008/093098, which is incorporated herein by reference in its entirety. Example gels that can be used in the methods and apparatus set forth herein include, but are not limited to those having a colloidal structure, such as agarose; polymer mesh structure, such as gelatin; or cross-linked polymer structure, such as polyacrylamide, SFA (see, for example, U.S. Patent Publ. No. 2011/0059865 A1, which is incorporated herein by reference in its entirety) or poly(N-(5-azidoacetamidylpentyl) acrylamide-co-acrylamide (PAZAM) (see, for example, U.S. Pat. No. 9,012,022, which is incorporated herein by reference in its entirety). Attachment via a bead can be achieved as exemplified in the description and cited references set forth previously herein.

In some examples, the features on the surface of an array substrate are non-contiguous, being separated by interstitial regions of the surface. Interstitial regions that have a substantially lower quantity or concentration of capture agents, compared to the features of the array, are advantageous. Interstitial regions that lack capture agents are particularly advantageous. For example, a relatively small amount or absence of capture moieties at the interstitial regions favors localization of target nucleic acids, and subsequently generated clusters, to desired features. In particular examples, the features can be concave features in a surface (e.g. wells) and the features can contain a gel material. The gel-containing features can be separated from each other by interstitial regions on the surface where the gel is at least substantially absent or, if present the gel is at least substantially incapable of supporting localization of nucleic acids. Methods and compositions for making and using substrates having gel containing features, such as wells, are set forth in U.S. Pat. No. 9,512,422, which is incorporated herein by reference in its entirety.

Target nucleic acids used in a method or composition of the present disclosure can be composed of DNA, RNA or analogs thereof. The source of the target nucleic acids can be genomic DNA, messenger RNA, or other nucleic acids from native sources. In some cases the target nucleic acids that are derived from such sources can be amplified prior to use in a method or composition herein. Any of a variety of known amplification techniques can be used including, but not limited to, polymerase chain reaction (PCR), rolling circle amplification (RCA), multiple displacement amplification (MDA), or random prime amplification (RPA). It will be understood that amplification of target nucleic acids prior to use in a method or composition set forth herein is optional. As such, target nucleic acids will not be amplified prior to use in some examples of the methods and compositions set forth herein. Target nucleic acids can optionally be derived from synthetic libraries. Synthetic nucleic acids can have native DNA or RNA compositions or can be analogs thereof.

Example biological samples from which target nucleic acids can be derived include, for example, those from a mammal such as a rodent, mouse, rat, rabbit, guinea pig, ungulate, horse, sheep, pig, goat, cow, cat, dog, primate, human or non-human primate; a plant such as Arabidopsis thaliana, corn, sorghum, oat, wheat, rice, canola, or soybean; an algae such as Chlamydomonas reinhardtii; a nematode such as Caenorhabditis elegans; an insect such as Drosophila melanogaster, mosquito, fruit fly, honey bee or spider; a fish such as zebrafish; a reptile; an amphibian such as a frog or Xenopus laevis; a dictyostelium discoideum; a fungi such as pneumocystis carinii, Takifugu rubripes, yeast, Saccharamoyces cerevisiae or Schizosaccharomyces pombe; or a plasmodium falciparum. Target nucleic acids can also be derived from a prokaryote such as a bacterium, Escherichia coli, staphylococci or mycoplasma pneumoniae; an archae; a virus such as Hepatitis C virus or human immunodeficiency virus; or a viroid. Target nucleic acids can be derived from a homogeneous culture or population of the above organisms or alternatively from a collection of several different organisms, for example, in a community or ecosystem.

Target nucleic acids need not be derived from natural sources and can instead be synthesized using known techniques. For example, gene expression probes or genotyping probes can be synthesized and used to create an array in the methods set forth herein.

In some examples, target nucleic acids can be obtained as fragments of one or more larger nucleic acids. Fragmentation can be carried out using any of a variety of techniques known in the art including, for example, nebulization, sonication, chemical cleavage, enzymatic cleavage, or physical shearing. Fragmentation may also result from use of a particular amplification technique that produces amplicons by copying only a portion of a larger nucleic acid. For example, PCR amplification produces fragments having a size defined by the length of the fragment between the flanking primers used for amplification.

A population of target nucleic acids, or amplicons thereof, can have an average strand length that is desired or appropriate for a particular application of the methods or compositions set forth herein. For example, the average strand length can be less than about 100,000 nucleotides, about 50,000 nucleotides, about 10,000 nucleotides, about 5,000 nucleotides, about 1,000 nucleotides, about 500 nucleotides, about 100 nucleotides, or about 50 nucleotides. Alternatively or additionally, the average strand length can be greater than about 10 nucleotides, about 50 nucleotides, about 100 nucleotides, about 500 nucleotides, about 1,000 nucleotides, about 5,000 nucleotides, about 10,000 nucleotides, about 50,000 nucleotides, or about 100,000 nucleotides. The average strand length for population of target nucleic acids, or amplicons thereof, can be in a range between a maximum and minimum value set forth above. It will be understood that amplicons generated at an amplification site (or otherwise made or used herein) can have an average strand length that is in a range between an upper and lower limit selected from those exemplified above.

In some cases a population of target nucleic acids can be produced under conditions or otherwise configured to have a maximum length for its members. For example, the maximum length for the members that are used in a method set forth herein or that are present in a particular composition can be less than about 100,000 nucleotides, about 50,000 nucleotides, about 10,000 nucleotides, about 5,000 nucleotides, about 1,000 nucleotides, about 500 nucleotides, about 100 nucleotides or about 50 nucleotides. Alternatively or additionally, a population of target nucleic acids, or amplicons thereof, can be produced under conditions or otherwise configured to have a minimum length for its members. For example, the minimum length for the members that are used in a method set forth herein or that are present in a particular composition can be more than about 10 nucleotides, about 50 nucleotides, about 100 nucleotides, about 500 nucleotides, about 1,000 nucleotides, about 5,000 nucleotides, about 10,000 nucleotides, about 50,000 nucleotides, or about 100,000 nucleotides. The maximum and minimum strand length for target nucleic acids in a population can be in a range between a maximum and minimum value set forth above. It will be understood that amplicons generated at an amplification site (or otherwise made or used herein) can have maximum and/or minimum strand lengths in a range between the upper and lower limits exemplified above.

In particular examples, the target nucleic acids are sized relative to the area of the amplification sites, for example, to facilitate kinetic exclusion. For example, the area for each of the sites of an array can be greater than the diameter of the excluded volume of the target nucleic acids in order to achieve kinetic exclusion. Taking, for example, examples that utilize an array of features on a surface, the area for each of the features can be greater than the diameter of the excluded volume of the target nucleic acids that are transported to the amplification sites. The excluded volume for a target nucleic acid and its diameter can be determined, for example, from the length of the target nucleic acid. Methods for determining the excluded volume of nucleic acids and the diameter of the excluded volume are described, for example, in U.S. Pat. No. 7,785,790; Rybenkov et al., Proc. Natl. Acad. Sci. U.S.A. 90: 5307-5311 (1993); Zimmerman et al., J. Mol. Biol. 222:599-620 (1991); or Sobel et al., Biopolymers 31:1559-1564 (1991), each of which is incorporated herein by reference in its entirety.

Amplification sites of an array can include a plurality of primers that are used to produce amplicons from a target nucleic acid. In some examples, the primers that are present at an amplification site can have a universal priming sequence that is complementary to a universal sequence that is present in an adapter sequence of each target nucleic acid. In particular examples, the plurality of primers can be attached to the amplification site. The primers can be attached to an amplification site as set forth above for capture nucleic acids.

As set forth previously herein, the features on the surface of an array substrate can be non-contiguous, being separated by interstitial regions of the surface. In particular examples, the interstitial regions will have a substantially lower quantity or concentration of primers, compared to the features of the array. Interstitial regions that lack primers are particularly advantageous. For example, a relatively small amount or absence of primers at the interstitial regions favors localization of amplicons to features on the surface of the array. This configuration creates a border for each array feature, thereby imparting the feature with a finite capacity for amplicons produced by amplification of a seeded target nucleic acid in methods set forth herein.

A method of the present disclosure can include reacting an amplification reagent to produce a plurality of amplification sites that each includes a clonal population of amplicons from an individual target nucleic acid that has seeded the site. In some examples the amplification reaction proceeds until a sufficient number of amplicons are generated to fill the capacity of the respective amplification site. Filling an already seeded site to capacity in this way excludes subsequent target nucleic acids from landing at the site, thereby producing a clonal population of amplicons at the site. Thus, it is desirable in some examples that the rate at which amplicons are generated to fill the capacity of amplification sites exceeds the rate at which the individual target nucleic acids are transported to the individual amplification sites respectively.

In some examples, apparent clonality can be achieved even if an amplification site is not filled to capacity prior to a second target nucleic acid arriving at the site. Under some conditions, amplification of a first target nucleic acid can proceed to a point that a sufficient number of copies are made to effectively outcompete or overwhelm production of copies from a second target nucleic acid that is transported to the site. For example, in an example that uses a bridge amplification process on a circular feature that is smaller than about 500 nm in diameter, it has been determined that after 14 cycles of exponential amplification for a first target nucleic acid, contamination from a second target nucleic acid at the same site will produce an insufficient number of contaminating amplicons to adversely impact sequencing-by-synthesis analysis on an Illumina sequencing platform.

As demonstrated by the above example, amplification sites in an array need not be entirely clonal in all examples. Rather, for some applications, an individual amplification site can be predominantly populated with amplicons from a first target nucleic acid and can also have a low level of contaminating amplicons from a second target nucleic acid. An array can have one or more amplification sites that have a low level of contaminating amplicons so long as the level of contamination does not have an unacceptable impact on a subsequent use of the array. For example, when the array is to be used in a detection application, an acceptable level of contamination would be a level that does not impact signal to noise or resolution of the detection technique in an unacceptable way. Accordingly, apparent clonality will generally be relevant to a particular use or application of an array made by the methods set forth herein. Example levels of contamination that can be acceptable at an individual amplification site for particular applications include, but are not limited to, at most about 0.1%, about 0.5%, about 1%, about 5%, about 10% or about 25% contaminating amplicons. An array can include one or more amplification sites having these example levels of contaminating amplicons. For example, up to about 5%, about 10%, about 25%, about 50%, about 75%, or even about 100% of the amplification sites in an array can have some contaminating amplicons.

In particular examples, a method of the present disclosure is carried out to simultaneously (i) transport target nucleic acids to amplification sites at an average transport rate, and (ii) amplify the target nucleic acids that are at the amplification sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. Accordingly, kinetic exclusion can be achieved in such examples by using a relatively slow rate of transport. For example, a sufficiently low concentration of target nucleic acids can be selected to achieve a desired average transport rate, lower concentrations resulting in slower average rates of transport. Alternatively or additionally, a high viscosity solution and/or presence of molecular crowding reagents (referred to herein as crowding agents) in the solution can be used to reduce transport rates. Examples of useful crowding reagents include, but are not limited to, polyethylene glycol (PEG), FICOLL®, dextran, or polyvinyl alcohol. Example crowding reagents and formulations are set forth in U.S. Pat. No. 7,399,590, which is incorporated herein by reference in its entirety. Another factor that can be adjusted to achieve a desired transport rate is the average size of the target nucleic acids.

In some examples of the methods, target nucleic acids can be transported, for example by diffusion or other process, to amplification sites, prior to initiation of amplification. In this case, kinetic exclusion can be achieved by exploiting a relatively slow rate of creating a first amplicon compared to the rate at which subsequent amplicons are made. For example, different rates of amplicon formation can be achieved by using a first primer for first amplicon formation that is initially in a temporary non-extendible state and other primers for subsequent amplicon formation that are in an extendible state throughout the amplification reaction. As such, a delay in the conversion of the first primer to an extendible state will cause a delay in first amplicon formation, whereas subsequent amplicon formation experiences no such delay. In this way, the average rate at which the subsequent amplicons are generated at the amplification sites exceeds the average rate at which the first amplicon is generated at the amplification sites.

A more detailed example of kinetic exclusion via differential rates of amplicon formation follows. An amplification site can include three subpopulations of primers attached thereto. The first subpopulation of primers functions to capture a target nucleic acid (via a capture sequence) and as a primer for first amplicon formation. The first subpopulation of primers is reversibly blocked from extension, for example, via a dideoxy nucleotide at the 3′ end. The second subpopulation of primers can have a P5 primer sequence and the third population of primers can have a P7 primer sequence. The primers of the first and second subpopulations do not include the dideoxy nucleotide and are therefore fully extension competent. Target nucleic acids can be constructed to include (from 5′ to 3′) a P7 primer binding sequence, one of several different target nucleotide sequences, a P5 primer binding sequence, and a capture sequence complement. Several different target nucleic acids can be hybridized to the first subpopulation of primers (via the capture sequences). The capture primers can then be converted to an extendible state, for example, by treatment with a polymerase under pyrophosphorolysis conditions (e.g., in the presence of excess pyrophosphate). Conditions can be used where, on average, only one of the capture primers will be converted to an extendible form during the time period in which subsequent amplicons are produced to fill the amplification site. Thus, although several potentially contaminating target nucleic acids may be present at an individual amplification site, kinetic exclusion will result in amplicon formation from only one of the target nucleic acids, thereby creating a clonal population of amplicons at the amplification site. For illustrative purposes, this example has been described with respect to a single amplification site, but it will be understood that the reaction can involve target nucleic attachment and amplification at an array of amplification sites.

Any of a variety of temporarily non-extendible primers can be used in a method set forth herein along with respective techniques and reagents for converting those primers to an extendible state. The example above describes use of a dideoxy nucleotide that is removed by pyrophosphorolysis. Other non-extendible nucleotides can be present on a primer and removed by pyrophosphorolysis. Furthermore, dideoxy nucleotides or other non-extendible nucleotides can be removed via other known techniques including, for example, exonuclease activity of a polymerase or other appropriate enzyme. In other examples, a primer can include a reversible terminator such as those used in terminator-based sequencing-by-synthesis methods. Examples of reversible terminators and techniques for their removal are described, for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497; U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,329,492; 7,211,414; 7,315,019; 7,405,281, and U.S. Patent Publ. No. 2008/0108082, each of which is incorporated herein by reference in its entirety.

Although the use of differentially active primers to cause different rates of first amplicon and subsequent amplicon formation has been exemplified above for an example where target nucleic acids are present at amplification sites prior to amplification, the method can also be carried out under conditions wherein the target nucleic acids are transported (e.g. via diffusion) to the amplification sites as amplification is occurring. Thus, kinetic exclusion can exploit both a relatively slow transport rate and a relatively slow production of first amplicon relative to subsequent amplicon formation. Thus, an amplification reaction set forth herein can be carried out such that target nucleic acids are transported from solution to amplification sites simultaneously with (i) the producing of a first amplicon, and (ii) the producing of the subsequent amplicons at other sites of the array. In particular examples, the average rate at which the subsequent amplicons are generated at the amplification sites can exceed the average rate at which the target nucleic acids are transported from the solution to the amplification sites. In some cases, a sufficient number of amplicons can be generated from a single target nucleic acid at an individual amplification site to fill the capacity of the respective amplification site. The rate at which amplicons are generated to fill the capacity of respective amplification sites can, for example, exceed the rate at which the individual target nucleic acids are transported from the solution to the amplification sites.

An amplification reagent that is used in a method set forth herein is preferably capable of rapidly making copies of target nucleic acids at amplification sites. One or more amplification reagents used in a method of the present disclosure will include a polymerase and nucleoside triphosphates (NTPs). Any of a variety of polymerases known in the art can be used, but in some examples it may be desirable to use a polymerase that is exonuclease negative. The NTPs can be deoxyribonucleoside triphosphates (dNTPs) for examples where DNA copies are made. The four native species of dNTPs, including dATP, dTTP, dGTP and dCTP, may be present in a DNA amplification reagent; however, analogs can be used if desired. The NTPs can be ribonucleoside triphosphates (rNTPs) for examples where RNA copies are made. The four native species of rNTPs, including rATP, rUTP, rGTP and rCTP, may be present in a RNA amplification reagent; however, analogs can be used if desired.

An amplification reagent can include further components that facilitate amplicon formation and in some cases increase the rate of amplicon formation. An example is a recombinase. A recombinase can facilitate amplicon formation by allowing repeated invasion/extension. More specifically, a recombinase can facilitate invasion of a target nucleic acid by the polymerase and extension of a primer by the polymerase using the target nucleic acid as a template for amplicon formation. This process can be repeated as a chain reaction where amplicons produced from each round of invasion/extension serve as templates in a subsequent round. The process can occur more rapidly than standard PCR since a denaturation cycle (e.g. via heating or chemical denaturation) is not required. As such, recombinase-facilitated amplification can be carried out isothermally. It is generally desirable to include ATP, or other nucleotides (or in some cases non-hydrolyzable analogs thereof) in a recombinase-facilitated amplification reagent to facilitate amplification. A mixture of recombinase and single stranded binding (SSB) protein is particularly useful as SSB can further facilitate amplification. Example formulations for recombinase-facilitated amplification include those sold commercially as TWISTAMP® kits by TwistDx (Cambridge, UK). Useful components of recombinase-facilitated amplification reagent and reaction conditions are set forth in U.S. Pat. Nos. 5,223,414 and 7,399,590, each of which is incorporated herein by reference in its entirety.

Another example of a component that can be included in an amplification reagent to facilitate amplicon formation, and in some cases to increase the rate of amplicon formation is a helicase. Helicase can facilitate amplicon formation by allowing a chain reaction of amplicon formation. The process can occur more rapidly than standard PCR since a denaturation cycle (e.g. via heating or chemical denaturation) is not required. As such, helicase-facilitated amplification can be carried out isothermally. A mixture of helicase and single stranded binding (SSB) protein is particularly useful as SSB can further facilitate amplification. Example formulations for helicase-facilitated amplification include those sold commercially as ISOAMP® kits from Biohelix (Beverly, Mass.). Further, examples of useful formulations that include a helicase protein are described in U.S. Pat. Nos. 7,399,590 and 7,829,284, each of which is incorporated herein by reference in its entirety.

Yet another example of a component that can be included in an amplification reagent to facilitate amplicon formation, and in some cases increase the rate of amplicon formation, is an origin binding protein.

The rate at which an amplification reaction occurs can be increased by increasing the concentration or amount of one or more of the active components of an amplification reaction. For example, the amount or concentration of polymerase, nucleoside triphosphates, primers, recombinase, helicase or SSB can be increased to increase the amplification rate. In some cases, the one or more active components of an amplification reaction that are increased in amount or concentration (or otherwise manipulated in a method set forth herein) are non-nucleic acid components of the amplification reaction.

The amplification rate can also be increased in a method set forth herein by adjusting the temperature. For example, the rate of amplification at one or more amplification sites can be increased by increasing the temperature at the site(s) up to a maximum temperature where reaction rate declines due to denaturation or other adverse events. Optimal or desired temperatures can be determined from known properties of the amplification components in use or empirically for a given amplification reaction mixture. Properties of primers used for amplification can also be adjusted to increase amplification rate. For example, the sequence and/or length of primers can be adjusted. Such adjustments can be made based on a priori predictions of primer melting temperature (Tm) or empirically.

Another option for increasing the rate of amplification at an amplification site is to increase the local concentration of one or more active components of the amplification reaction at the amplification site. The active components can include one or more non-nucleic acid components. In some examples, one or more active components of an amplification reaction can be attracted to an amplification site using electrical manipulations such as electrophoresis, isotachophoresis, direct pulsing of current or voltage or the like. Alternatively or additionally, one or more of the amplification components can include an affinity tag that recruits it to the amplification site. An affinity tag can be charged such that electrical manipulations will attract an appropriately tagged component to an amplification site. Non-charged affinity tags can be used as well. For example, any of a variety of ligands or receptors known in the art, such as those set forth herein as examples of capture agents, can be used as affinity tags for a component of an amplification reaction. As is the case for capture agents used for nucleic acids, an amplification site can include a binding partner for an affinity tag of an amplification component. Thus, the local concentration of the affinity tagged amplification component can be increased due to interaction with the appropriate partner at the amplification site. In particular examples where the amplification site is a surface of a substrate, a binding partner for an affinity tag can be attached to the surface.

Furthermore, magnetic or optical forces can be used to increase the local concentration of amplification reagents. In such cases, one or more amplification reagents can include a magnetic tag or optical tag that can be manipulated by such forces.

The rate at which an amplification reaction occurs can be increased by increasing the activity of one or more amplification reagent. For example, a cofactor that increases the extension rate of a polymerase can be added to a reaction where the polymerase is in use. In some examples, metal cofactors, such as magnesium, zinc or manganese, can be added to a polymerase reaction, or, in other examples, betaine can be added.

In some examples of the methods set forth herein, it is desirable to use a population of target nucleic acids that is double stranded. It has been surprisingly observed that amplicon formation at an array of sites under kinetic exclusion conditions is efficient for double stranded target nucleic acids. For example, a plurality of amplification sites having clonal populations of amplicons can be more efficiently produced from double stranded target nucleic acids (compared to single stranded target nucleic acids at the same concentration) in the presence of recombinase and single stranded binding protein. Nevertheless, it will be understood that single stranded target nucleic acids can be used in some examples of the methods set forth herein.

A method set forth herein can use any of a variety of amplification techniques. Example techniques that can be used include, but are not limited to, polymerase chain reaction (PCR), rolling circle amplification (RCA), multiple displacement amplification (MDA), or random prime amplification (RPA). In some examples the amplification can be carried out in solution, for example, when the amplification sites are capable of containing amplicons in a volume having a desired capacity. Preferably, an amplification technique used under conditions of kinetic exclusion in a method of the present disclosure will be carried out on solid phase. For example, one or more primers used for amplification can be attached to a solid phase at the amplification site. In PCR examples, one or both of the primers used for amplification can be attached to a solid phase. Formats that utilize two species of primer attached to the surface are often referred to as bridge amplification because double stranded amplicons form a bridge-like structure between the two surface-attached primers that flank the template sequence that has been copied. Example reagents and conditions that can be used for bridge amplification are described, for example, in U.S. Pat. No. 5,641,658; U.S. Patent Publ. No. 2002/0055100; U.S. Pat. No. 7,115,400; U.S. Patent Publ. No. 2004/0096853; U.S. Patent Publ. No. 2004/0002090; U.S. Patent Publ. No. 2007/0128624; and U.S. Patent Publ. No. 2008/0009420, each of which is incorporated herein by reference in its entirety. Solid-phase PCR amplification can also be carried out with one of the amplification primers attached to a solid support and the second primer in solution. An example format that uses a combination of a surface attached primer and soluble primer is emulsion PCR as described, for example, in Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003), WO 05/010145, or U.S. Patent Publ. Nos. 2005/0130173 or 2005/0064460, each of which is incorporated herein by reference in its entirety. Emulsion PCR is illustrative of the format and it will be understood that for purposes of the methods set forth herein the use of an emulsion is optional, and indeed, for several examples, an emulsion is not used. The above-exemplified PCR techniques can be modified for non-cyclic amplification (e.g., isothermal amplification) using components exemplified elsewhere herein for facilitating or increasing the rate of amplification. Accordingly, the above-exemplified PCR techniques can be used under kinetic exclusion conditions.

RCA techniques can be modified for use in a method of the present disclosure. Example components that can be used in an RCA reaction and principles by which RCA produces amplicons are described, for example, in Lizardi et al., Nat. Genet. 19:225-232 (1998) and U.S. Patent Publ. No. 2007/0099208 A1, each of which is incorporated herein by reference in its entirety. Primers used for RCA can be in solution or attached to a solid support surface at an amplification site. The RCA techniques exemplified in the above references can be modified in accordance with teaching herein, for example, to increase the rate of amplification to suit particular applications. Thus, RCA techniques can be used under kinetic exclusion conditions.

MDA techniques can be modified for use in a method of the present disclosure. Some basic principles and useful conditions for MDA are described, for example, in Dean et al., Proc Natl. Acad. Sci. USA 99:5261-66 (2002); Lage et al., Genome Research 13:294-307 (2003); Walker et al., Molecular Methods for Virus Detection, Academic Press, Inc., 1995; Walker et al., Nucl. Acids Res. 20:1691-96 (1992); U.S. Pat. Nos. 5,455,166; 5,130,238; and 6,214,587, each of which is incorporated herein by reference in its entirety. Primers used for MDA can be in solution or attached to a solid support surface at an amplification site. The MDA techniques exemplified in the above references can be modified in accordance with teaching herein, for example, to increase the rate of amplification to suit particular applications. Accordingly, MDA techniques can be used under kinetic exclusion conditions.

In particular examples, a combination of the above-exemplified amplification techniques can be used to make an array under kinetic exclusion conditions. For example, RCA and MDA can be used in a combination wherein RCA is used to generate a concatameric amplicon in solution (e.g. using solution-phase primers). The amplicon can then be used as a template for MDA using primers that are attached to a solid support surface at an amplification site. In this example, amplicons produced after the combined RCA and MDA steps will be attached to the surface of the amplification site.

As exemplified with respect to several of the examples above, a method of the present disclosure need not use a cyclical amplification technique. For example, amplification of target nucleic acids can be carried out at amplification sites absent a denaturation cycle. Example denaturation cycles include introduction of chemical denaturants to an amplification reaction and/or increasing the temperature of an amplification reaction. Thus, amplifying of the target nucleic acids need not include replacing the amplification solution with a chemical reagent that denatures the target nucleic acids and the amplicons. Similarly, amplifying of the target nucleic acids need not include heating the solution to a temperature that denatures the target nucleic acids and the amplicons. Accordingly, amplifying of target nucleic acids at amplification sites can be carried out isothermally for the duration of a method set forth herein. Indeed an amplification method set forth herein can occur without one or more cyclic manipulations that are carried out for some amplification techniques under standard conditions. Furthermore, in some standard solid phase amplification techniques, a wash is carried out after target nucleic acids are loaded onto a substrate and before amplification is initiated. However, in examples of the present methods, a wash step need not be carried out between transport of target nucleic acids to reaction sites and amplification of the target nucleic acids at the amplification sites. Instead, transport (e.g., via diffusion) and amplification are allowed to occur simultaneously to provide for kinetic exclusion.

In some examples it may be desirable to repeat an amplification cycle that occurs under kinetic exclusion conditions. Thus, although copies of a target nucleic acid can be made at an individual amplification site via kinetic exclusion amplification without cyclic manipulations involving chemical denaturants or heat applications, an array of amplification sites can be treated cyclically to increase the number of sites that contain amplicons and/or the number of amplicons at each site after each cycle of kinetic exclusion amplification. In one or more examples described herein with reference to FIGS. 11-14, a secondary amplification or boost may be performed after the initial exclusion amplification by flowing a fresh, target-less solution that includes reagents (e.g., active components) without target nucleic acids over the amplification sites. The reagents in the target-less solution may increase the number of amplicons in the clonal clusters at the amplification sites. Due to the lack of target nucleic acids in the target-less solution, the reagent may not cause additional seeding of target nucleic acids at the amplification sites. In particular examples, the amplification conditions can be modified from one cycle to the next. For example, one or more of the conditions set forth above for altering the rate of transport or altering the rate of amplification can be adjusted between cycles. As such, the rate of transport can be increased from cycle to cycle, the rate of transport can be decreased from cycle to cycle, the rate of amplification can be increased from cycle to cycle, or the rate of amplification can be decreased from cycle to cycle.

A method set forth herein can be modified to use electric field (e-field) assisted transport of target nucleic acids to amplification sites of the array. For example, each amplification site of an array can be electrically coupled to a power source to produce an electric charge that attracts target nucleic acids. In one configuration, a positive charge at the amplification sites can attract nucleic acids via the negatively charged sugar-phosphate backbone. Example methods and apparatus for using e-field assist to attract nucleic acids to sites of an array are described in U.S. Patent Publ. No. 2009/0032401 A1, which is incorporated herein by reference in its entirety. E-field assist can be used in a method of the present disclosure, for example, under conditions where a plurality of different target nucleic acids is in solution such that the nucleic acid targets have fluidic access to the array of amplification sites during each amplification step. The charge at each amplification site can be adjusted to achieve kinetic exclusion. Additionally or alternatively to adjusting the charge, other conditions set forth herein for altering target nucleic acid transport rates or for altering amplification rates can be adjusted to achieve kinetic exclusion. Accordingly, the charge at amplification sites of an array can be adjusted to attract target nucleic acids while amplification simultaneously occurs at various amplification sites of the array, wherein the average amplification rate exceeds the average rate at which the target nucleic acids are transported (i.e., under e-field assisted transport) to the amplification sites.

In particular examples that utilize e-field assisted transport of target nucleic acids to amplification sites, the e-field can be consistently applied throughout the course of the amplification reaction. Alternatively, the e-field can be changed (e.g., increased or decreased) as the amplification reaction progresses and as amplification sites fill with amplicons. For example, increasing the e-field can provide the benefit of increasing the number of amplification sites that acquire a target nucleic acid (that is in turn amplified to produce a clonal population of amplicons at each of the sites). The rate at which the e-field is increased, and the amplitude range for the increase, can be selected to balance the increasing rate of target nucleic acid transport over time with the increasing number of amplification sites that have become effectively filled over that same period of time. Again, depending upon the application of the arrays produced by the method, effective filling may be the point at which the amplification sites have become filled to capacity with copies of a first target nucleic acid, thereby preventing amplification of any secondary target nucleic acids at that site. Alternatively, effective filling can be the point at which amplification of a secondary target nucleic acid at a particular amplification site would produce a sufficiently low fraction of contaminating amplicons to be considered negligible or otherwise acceptable for the desired use of the array.

Generally, e-field assist allows a further level of control over transport of target nucleic acids to one or more amplification sites of an array. Although the use of e-field assist has been exemplified above in the context of transporting target nucleic acids to an array of amplification sites simultaneously with amplification occurring at various sites of the array, in alternative examples, e-field assist can be used to transport target nucleic acids to amplification sites prior to initiation of amplification at the sites. E-field assist can be used in a method or composition set forth herein to transport target biomolecules other than target nucleic acids to a site of interest, such as to a feature of an array.

In particular examples, an e-field can be applied to all of the amplification sites of an array at least substantially uniformly. Thus, target nucleic acids that are in solution will have an equal probability of being transported to any given amplification site. In an alternative example, an e-field can be applied to only a subset of the amplification sites that are present in an array. In this way, e-field assist can be used to selectively fill some sites over others. Furthermore, if desired, an attractive charge can be applied at a first subset of amplification sites in order to transport target nucleic acids to the first subset of sites and in the meantime a repellant charge can be applied to a second subset of amplification sites to inhibit target nucleic acids from being transported to those sites or to remove (e.g., via desorption or degradation) target nucleic acids from the second subset of sites. Similarly a repellant charge can be applied to interstitial regions of an array to inhibit target nucleic acids from being transported to the interstitial regions or to remove (e.g., via desorption or degradation) target nucleic acids from the interstitial regions as set forth in further detail below and in Example III.

In particular examples, interstitial regions of an array can be electrically coupled to a power source to produce an electric charge that inhibits binding of or removes target nucleic acids or other biomolecules. In one configuration, a negative charge at the interstitial regions can repel nucleic acids via the negatively charged sugar-phosphate backbone. Alternatively or additionally, the charge in the interstitial region can be used to create surface-localized pH changes that electrochemically damage nucleic acids and biomolecules.

E-field repulsion can be used in a method of the present disclosure, for example, under conditions where a plurality of different target nucleic acids is in solution such that the nucleic acid targets have fluidic access to the array of amplification sites during each amplification step. The charge at the interstitial regions of an array can be adjusted to repel nucleic acids (e.g., by removal or binding inhibition) while the nucleic acids are captured at the features of the array and, optionally, amplified at the features under kinetic exclusion conditions. Additionally or alternatively to adjusting the charge, other conditions set forth herein for altering target nucleic acid transport rates to features or for altering amplification rates can be adjusted to achieve kinetic exclusion. Accordingly, the charge at interstitial regions of an array can be adjusted to repel target nucleic acids while amplification simultaneously occurs at various amplification sites of the array, wherein the average amplification rate exceeds the average rate at which the target nucleic acids are transported to the amplification sites. Accordingly, electric field repulsion at interstitial regions can be used in combination with other methods set forth herein for transporting nucleic acids (or other biomolecules) to features of an array and achieving kinetic exclusion.

Electric field repulsion at interstitial regions using methods and apparatus set forth herein can provide an advantage of improving specific localization of nucleic acids (or other biomolecules) at the features instead of at interstitial regions. Such advantages can follow whether the repulsion works via a mechanism of charge repulsion to inhibit binding of nucleic acids or other biomolecules, via surface-localized electrochemical damage of nucleic acids and biomolecules or via other mechanisms. Electric field repulsion at interstitial regions can be used to improve specific localization of nucleic acids or other biomolecules to features of interest, particularly when the features of interest have a height taller than the reach of surface-localized electrochemical damage.

Some examples can utilize electric field assisted transport of nucleic acids (or other biomolecules) to the features of an array in combination with electric field assisted repulsion of the nucleic acids (or other biomolecules) from the interstitial regions of the array. The attractive electric field and repulsive electric field can be applied simultaneously to the array or the two fields can be applied separately. For example, the two fields can be applied separately such that the fields are applied in alternate repetitions (e.g., the attractive field can be applied to the features while the repulsive field is off, then the attractive field can be turned off while the repulsive field is applied to the interstitial regions, and this sequence can be repeated one or more times).

An electric field can be applied across a region of an array and an electrolyte or it can be applied across the region of the array and a second surface. For example, FIG. 4(a) shows a configuration where an electric field can be applied across an interstitial region of an array and an electrolyte and FIG. 4(b) shows a configuration where an electric field can be applied across an interstitial region of an array and a second surface. Similar configurations can be used to apply attractive fields to features of an array. Furthermore, the electric fields, whether applied to a feature or interstitial region, can be created by application of an alternating current (AC) or a direct current (DC) to the appropriate region of the array.

Accordingly, the disclosure provides a method for creating a patterned surface of biomolecules, wherein the method can include (a) providing a reagent including (i) an array having non-contiguous features on a surface, the features being separated by interstitial regions of the surface, and (ii) a solution having a plurality of different target biomolecules; and (b) reacting the reagent to transport the biomolecules to the features and attach an individual biomolecule to each of the features, wherein an electric field is applied to the interstitial regions to repel the biomolecules from the interstitial regions. Particularly useful biomolecules for use in the method are nucleic acids. The nucleic acids can be amplified at the features in this method under kinetic exclusion conditions, such as those that are set forth elsewhere herein. In some examples that use electric fields, a substrate used for an array can include a layer of transparent electrical conductor. The layer of electrical conductor may be used as an electrode to connect an electrical source, such as a battery or a signal generator. If desired, a feature of an array (e.g., inner surfaces of a well in an array of wells) can contain an exposed or an insulated conductive layer, wherein a voltage across the conductive layers can be used to manipulate the force on a nucleic acid and/or amplification reagents to control the rate of transport to the site, capture at the site, removal from the site and/or amplification at the site. In particular examples, an electric field can be applied on the outer surfaces of a well such that the electric field that penetrates the vessel walls induces an electrical force on reagents within the vessel, providing a degree of control over the rates of transport, capture, removal and/or amplification.

An array of the present disclosure, for example, having been produced by a method set forth herein, can be used for any of a variety of applications. A particularly useful application is nucleic acid sequencing. One example is sequencing-by-synthesis (SBS). In SBS, extension of a nucleic acid primer along a nucleic acid template (e.g., a target nucleic acid or amplicon thereof) is monitored to determine the sequence of nucleotides in the template. The underlying chemical process can be polymerization (e.g., as catalyzed by a polymerase enzyme). In a particular polymerase-based SBS example, fluorescently labeled nucleotides are added to a primer (thereby extending the primer) in a template dependent fashion such that detection of the order and type of nucleotides added to the primer can be used to determine the sequence of the template. A plurality of different templates at different sites of an array set forth herein can be subjected to an SBS technique under conditions where events occurring for different templates can be distinguished due to their location in the array.

Flow cells provide a convenient format for housing an array that is produced by the methods of the present disclosure and that is subjected to an SBS or other detection technique that involves repeated delivery of reagents in cycles. For example, to initiate a first SBS cycle, one or more labeled nucleotides, DNA polymerase, etc., can be flowed into/through a flow cell that houses an array of nucleic acid templates. Those sites of an array where primer extension causes a labeled nucleotide to be incorporated can be detected. Optionally, the nucleotides can further include a reversible termination property that terminates further primer extension once a nucleotide has been added to a primer. For example, a nucleotide analog having a reversible terminator moiety can be added to a primer such that subsequent extension cannot occur until a deblocking agent is delivered to remove the moiety. Thus, for examples that use reversible termination, a deblocking reagent can be delivered to the flow cell (before or after detection occurs). Washes can be carried out between the various delivery steps. The cycle can then be repeated n times to extend the primer by n nucleotides, thereby detecting a sequence of length n. Example SBS procedures, fluidic systems and detection platforms that can be readily adapted for use with an array produced by the methods of the present disclosure are described, for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497; U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,329,492; 7,211,414; 7,315,019; 7,405,281, and U.S. Patent Publ. No. 2008/0108082, each of which is incorporated herein by reference in its entirety.

Other sequencing procedures that use cyclic reactions can be used, such as pyrosequencing. Pyrosequencing detects the release of inorganic pyrophosphate (PPi) as particular nucleotides are incorporated into a nascent nucleic acid strand (Ronaghi, et al., Analytical Biochemistry 242(1), 84-9 (1996); Ronaghi, Genome Res. 11(1), 3-11 (2001); Ronaghi et al. Science 281(5375), 363 (1998); U.S. Pat. Nos. 6,210,891; 6,258,568 and 6,274,320, each of which is incorporated herein by reference in its entirety). In pyrosequencing, released PPi can be detected by being immediately converted to adenosine triphosphate (ATP) by ATP sulfurylase, and the level of ATP generated can be detected via luciferase-produced photons. Thus, the sequencing reaction can be monitored via a luminescence detection system. Excitation radiation sources used for fluorescence based detection systems are not necessary for pyrosequencing procedures. Useful fluidic systems, detectors and procedures that can be used for application of pyrosequencing to arrays of the present disclosure are described, for example, in U.S. Pat. No. 9,096,899, U.S. Patent Publ. No. 2005/0191698 A1, U.S. Pat. Nos. 7,595,883, and 7,244,559, each of which is incorporated herein by reference in its entirety.

Sequencing-by-ligation reactions are also useful including, for example, those described in Shendure et al. Science 309:1728-1732 (2005); U.S. Pat. Nos. 5,599,675; and 5,750,341, each of which is incorporated herein by reference in its entirety. Some examples can include sequencing-by-hybridization procedures as described, for example, in Bains et al., Journal of Theoretical Biology 135(3), 303-7 (1988); Drmanac et al., Nature Biotechnology 16, 54-58 (1998); Fodor et al., Science 251(4995), 767-773 (1995); and WO 1989/10977, each of which is incorporated herein by reference in its entirety. In both sequencing-by-ligation and sequencing-by-hybridization procedures, target nucleic acids (or amplicons thereof) that are present at sites of an array are subjected to repeated cycles of oligonucleotide delivery and detection. Fluidic systems for SBS methods as set forth herein or in references cited herein can be readily adapted for delivery of reagents for sequencing-by-ligation or sequencing-by-hybridization procedures. The oligonucleotides may be fluorescently labeled and detected using fluorescence detectors similar to those described with regard to SBS procedures herein or in references cited herein.

Some examples can utilize methods involving the real-time monitoring of DNA polymerase activity. For example, nucleotide incorporations can be detected through fluorescence resonance energy transfer (FRET) interactions between a fluorophore-bearing polymerase and γ-phosphate-labeled nucleotides, or with zeromode waveguides (ZMWs). Techniques and reagents for FRET-based sequencing are described, for example, in Levene et al. Science 299, 682-686 (2003); Lundquist et al. Opt. Lett. 33, 1026-1028 (2008); Korlach et al. Proc. Natl. Acad. Sci. USA 105, 1176-1181 (2008), each of which is incorporated herein by reference in its entirety.

Some SBS examples include detection of a proton released upon incorporation of a nucleotide into an extension product. For example, sequencing based on detection of released protons can use an electrical detector, and associated techniques are commercially available from Ion Torrent (Guilford, Conn., a Life Technologies subsidiary) or sequencing methods and systems are described in U.S. Patent Publ. No. 2009/0026082 A1; U.S. Patent Publ. No. 2009/0127589 A1; U.S. Patent Publ. No. 2010/0137143 A1; or U.S. Patent Publ. No. 2010/0282617 A1, each of which is incorporated herein by reference in its entirety. Methods set forth herein for amplifying target nucleic acids using kinetic exclusion can be readily applied to substrates used for detecting protons. More specifically, methods set forth herein can be used to produce clonal populations of amplicons at the sites of the arrays that are used to detect protons.

Another useful application for an array of the present disclosure, for example, having been produced by a method set forth herein, is gene expression analysis. Gene expression can be detected or quantified using RNA sequencing techniques, such as those referred to as digital RNA sequencing. RNA sequencing techniques can be carried out using sequencing methodologies known in the art such as those set forth above. Gene expression can also be detected or quantified using hybridization techniques carried out by direct hybridization to an array or using a multiplex assay, the products of which are detected on an array. An array of the present disclosure, for example, having been produced by a method set forth herein, can also be used to determine genotypes for a genomic DNA sample from one or more individual. Example methods for array-based expression and genotyping analysis that can be carried out on an array of the present disclosure are described in U.S. Pat. Nos. 7,582,420; 6,890,741; 6,913,884 or 6,355,431 or U.S. Patent Publ. Nos. 2005/0053980 A1; 2009/0186349 A1 or 2005/0181440 A1, each of which is incorporated herein by reference in its entirety.

An advantage of the methods set forth herein is that they provide for rapid and efficient creation of arrays from any of a variety of nucleic acid libraries. Accordingly, the present disclosure provides integrated systems capable of making an array using one or more of the methods set forth herein and further capable of detecting nucleic acids on the arrays using techniques known in the art such as those exemplified above. Thus, an integrated system of the present disclosure can include fluidic components capable of delivering amplification reagents to an array of amplification sites such as pumps, valves, reservoirs, fluidic lines and the like. A particularly useful fluidic component is a flow cell. A flow cell can be configured and/or used in an integrated system to create an array of the present disclosure and to detect the array. Example flow cells are described, for example, in U.S. Patent Publ. No. 2010/0111768 A1 and U.S. Pat. No. 8,951,781, each of which is incorporated herein by reference in its entirety. As exemplified for flow cells, one or more of the fluidic components of an integrated system can be used for an amplification method and for a detection method. Taking a nucleic acid sequencing example, one or more of the fluidic components of an integrated system can be used for an amplification method set forth herein and for the delivery of sequencing reagents in a sequencing method such as those exemplified above. Alternatively, an integrated system can include separate fluidic systems to carry out amplification methods and to carry out detection methods. Examples of integrated sequencing systems that are capable of creating arrays of nucleic acids and also determining the sequence of the nucleic acids include, without limitation, the MISEQ® instrument platform (Illumina, Inc., San Diego, Calif.) and devices described in the U.S. Pat. No. 8,951,781 (referenced above). Such devices can be modified to make arrays using kinetic exclusion in accordance with the guidance set forth herein.

A system capable of carrying out a method set forth herein need not be integrated with a detection device. Rather, a stand-alone system or a system integrated with other devices is also possible. Fluidic components similar to those exemplified above in the context of an integrated system can be used in such examples.

A system capable of carrying out a method set forth herein, whether integrated with detection capabilities or not, can include a system controller that is capable of executing a set of instructions to perform one or more methods, techniques or processes set forth herein. For example, the instructions can direct the performance of steps for creating an array under kinetic exclusion conditions. Optionally, the instructions can further direct the performance of steps for detecting nucleic acids using methods set forth previously herein. A useful system controller may include any processor-based or microprocessor-based system, including systems using microcontrollers, reduced instruction set computers (RISC), application specific integrated circuits (ASICs), field programmable gate array (FPGAs), logic circuits, and any other circuit or processor capable of executing functions described herein. A set of instructions for a system controller may be in the form of a software program. As used herein, the terms “software” and “firmware” are interchangeable, and include any computer program stored in memory for execution by a computer, including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory. The software may be in various forms such as system software or application software. Further, the software may be in the form of a collection of separate programs, or a program module within a larger program or a portion of a program module. The software also may include modular programming in the form of object-oriented programming.

Several applications for arrays of the present disclosure have been exemplified above in the context of ensemble detection, wherein multiple amplicons present at each amplification site are detected together. In alternative examples, a single nucleic acid, whether a target nucleic acid or amplicon thereof, can be detected at each amplification site. For example, an amplification site can be configured to contain a single nucleic acid molecule having a target nucleotide sequence that is to be detected and a plurality of filler nucleic acids. In this example, the filler nucleic acids function to fill the capacity of the amplification site and they are not necessarily intended to be detected. The single molecule that is to be detected can be detected by a method that is capable of distinguishing the single molecule in the background of the filler nucleic acids. Any of a variety of single molecule detection techniques can be used including, for example, modifications of the ensemble detection techniques set forth above to detect the sites at increased gain or using more sensitive labels. Other examples of single molecule detection methods that can be used are set forth in U.S. Patent Publ. No. 2011/0312529 A1; U.S. Pat. No. 9,279,154; and U.S. Patent Publ. No. 2013/0085073 A1, each of which is incorporated herein by reference in its entirety.

An array useful for single molecule nucleic acid detection can be created using one or more of the methods set forth herein with the following modifications. A plurality of different target nucleic acids can be configured to include both a target nucleotide sequence that is to be detected and one or more filler nucleotide sequences that are to be amplified to create filler amplicons. The plurality of different target nucleic acids can be included in an amplification reagent, such as those set forth elsewhere herein, and reacted with an array of amplification sites under kinetic exclusion conditions such that the filler nucleotide sequence(s) fills the amplification sites. Example configurations that can be used to allow the filler sequences to be amplified while prohibiting amplification of the target sequence include, for example, a single target molecule having a first region with filler sequences flanked by binding sites for amplification primers present at the amplification site and a second region having a target sequence outside of the flanked region. In another configuration, a target nucleic acid can include separate molecules or strands that carry the target sequence and filler sequence(s), respectively. The separate molecules or strands can be attached to a particle or formed as arms of a nucleic acid dendrimer or other branched structure.

In a particular example, an array having amplification sites that each contain both filler sequences and a target sequence can be detected using a primer extension assay or sequencing-by-synthesis technique. In such cases, specific extension can be achieved at the target nucleotide sequence as opposed to at the large amount of filler sequence by use of appropriately placed primer binding sites. For example, binding sites for sequencing primers can be placed upstream of the target sequence and can be absent from any of the filler sequences. Alternatively or additionally, the target sequence can include one or more non-native nucleotide analogs that are not capable of hydrogen bonding to standard nucleotides. The non-native nucleotide(s) can be placed downstream of the primer binding site (e.g., in the target sequence or in a region intervening the target sequence and the primer biding site) and, as such, will prevent extension or sequencing-by-synthesis until an appropriate nucleotide partner (i.e., one capable of hydrogen bonding to the non-native analog(s) in the target sequence) is added. The nucleotide analogs isocytosine (isoC) and isoguanine (isoG) are particularly useful since they pair specifically with each other but not with other standard nucleotides used in most extension and sequencing-by-synthesis techniques. A further benefit of using isoC and/or isoG in a target sequence or upstream of the target sequence is to prevent unwanted amplification of the target sequence during amplification steps by omitting the respective partner from the nucleotide mixture used for amplification.

It will be understood that an array of the present disclosure, for example, having been produced by a method set forth herein, need not be used for a detection method. Rather, the array can be used to store a nucleic acid library. Accordingly, the array can be stored in a state that preserves the nucleic acids therein. For example, an array can be stored in a desiccated state, frozen state (e.g., in liquid nitrogen), or in a solution that is protective of nucleic acids. Alternatively or additionally, the array can be used to replicate a nucleic acid library. For example, an array can be used to create replicate amplicons from one or more of the sites on the array.

Several examples have been exemplified herein with regard to transporting target nucleic acids to amplification sites of an array and making copies of the captured target nucleic acids at the amplification sites. Similar methods can be used for non-nucleic acid target molecules. Thus, methods set forth herein can be used with other target molecules in place of the exemplified target nucleic acids. For example, a method of the present disclosure can be carried out to transport individual target molecules from a population of different target molecules. Each target molecule can be transported to (and in some cases captured at) an individual site of an array to initiate a reaction at the site of capture. The reaction at each site can, for example, produce copies of the captured molecule or the reaction can alter the site to isolate or sequester the captured molecule. In either case, the end result can be sites of the array that are each pure with respect to the type of target molecule that is present from a population that contained different types of target molecules.

In particular examples that use target molecules other than nucleic acids, a library of different target molecules can be made using a method that exploits kinetic exclusion. For example, a target molecule array can be made under conditions where sites of the array are randomly seeded with target molecules from a solution and copies of the target molecule are generated to fill each of the seeded sites to capacity. In accordance with the kinetic exclusion methods of the present disclosure, the seeding and copying processes can proceed simultaneously under conditions where the rate at which copies are made exceeds the seeding rate. As such, the relatively rapid rate at which copies are made at a site that has been seeded by a first target molecule will effectively exclude a second target molecule from seeding the site. In some cases, seeding of a target molecule will initiate a reaction that fills a site to capacity by a process other than copying of the target molecule. For example, the capture of a target molecule at a site can initiate a chain reaction that eventually renders the site incapable of capturing a second target molecule. The chain reaction can occur at a rate that exceeds the rate at which the target molecules are captured, thereby occurring under conditions of kinetic exclusion.

As exemplified for target nucleic acids, kinetic exclusion when applied to other target molecules can exploit a relatively slow rate for initiating a repetitive reaction (e.g., a chain reaction) at a site of an array versus a relatively rapid rate for continuing the repetitive reaction once initiated. In the example of the previous paragraph, kinetic exclusion occurs due to the relatively slow rate of target molecule seeding (e.g., relatively slow diffusion) versus the relatively rapid rate at which a reaction occurs, for example, to fill the site with copies of the target molecule seed. In another example, kinetic exclusion can occur due to a delay in the formation of a first copy of a target molecule that has seeded a site (e.g., delayed or slow activation) versus the relatively rapid rate at which subsequent copies are made to fill the site. In this example, an individual site may have been seeded with several different target molecules. However, first copy formation for any given target molecule can be activated randomly such that the average rate of first copy formation is relatively slow compared to the rate at which subsequent copies are generated. In this case, although an individual site may have been seeded with several different target molecules, kinetic exclusion will allow only one of those target molecules to be copied.

Accordingly, the present disclosure provides a method for making an array of molecules that can include (a) providing a reagent including (i) an array of sites, and (ii) a solution having a plurality of different target molecules, wherein the number of the target molecules in the solution exceeds the number of sites in the array, wherein the different target molecules have fluidic access to the plurality of sites, and wherein each of the sites comprises a capacity for several target molecules in the plurality of different target molecules; and (b) reacting the reagent to produce a plurality of sites that each have a single target molecule from the plurality or to produce a plurality of sites that each have a pure population of copies from an individual target molecule from the solution, wherein the reacting includes simultaneously (i) transporting the different molecules to the sites at an average transport rate, and (ii) initiating a reaction that fills the site to capacity at an average reaction rate, wherein the average reaction rate exceeds the average transport rate. In some examples, step (b) can instead be carried out by reacting the reagent to produce a plurality of sites that each have a single target molecule from the plurality or to produce a plurality of sites that each have a pure population of copies from an individual target molecule from the solution, wherein the reacting includes (i) initiating a repetitive reaction (e.g., a chain reaction) to form a product from the target molecule at each of the sites, and (ii) continuing the reaction at each of the sites to form subsequent products, wherein the average rate at which the reaction occurs at the sites exceeds the average rate at which the reaction is initiated at the sites.

In the non-nucleic acid examples above, the target molecule can be an initiator of a repetitive reaction that occurs at each site of the array. For example, the repetitive reaction can form a polymer that precludes other target molecules from occupying the site. Alternatively, the repetitive reaction can form one or more polymers that constitute molecular copies of a target molecule that was transported to the site.

The following examples are intended to illustrate but not limit the present inventive subject matter.

EXAMPLE I

Super-Poisson Formation of Cluster Arrays on Flow Cells

This example describes a method to achieve super-Poisson formation of a cluster array on a flow cell for an Illumina (San Diego, Calif.) sequencing platform. The method described here is a process to capture a library element (e.g., a genome fragment) on a feature and to simultaneously clonally amplify the library element. A key feature of the process in this example is to control the rate of capture versus the rate of amplification and to do so in a homogenous process. Many prior processes developed for high density seeding of Illumina flow cells, separate the capture of the library element from the clonal amplification process. In this example, the capture event initiates a clonal amplification event on the feature.

A patterned flow cell is prepared as follows. Glass flow cells (Illumina, Inc., San Diego, Calif.) are coated with gold patches using a lift-off approach. Briefly, a photoresist layer is evenly coated over the surface of the glass flow cell and patches of the photoresist are removed by photolithography to expose patches of the glass surface. A layer of gold is then deposited on the surface to form a continuous thin film over the photoresist regions and glass patches. Gold can be deposited using e-beam evaporation or sputtering as set forth in Thornton, Ann. Rev. Mater. Sci. 7:239-60 (1977), which is incorporated herein by reference in its entirety. The photoresist layer is then removed by acetone lift off to leave gold patches that are circular in shape, having a diameter that is less than 1 micron, and being surrounded by interstitial regions of the glass surface. The gold patterned flow cell is then coated with silane-free acrylamide (SFA) as described in WO 2008/093098 (which is incorporated herein). P5 and P7 primers are grafted to the polymerized SFA via a nitrobenzyl UV cleavable moiety (Glenn Research, Sterling, Va.). The flow cell is positioned on a UV (302 nm) light source such that the gold patches create a mask for primers attached over the patches while any primers attached over interstitial regions are cleaved due to UV light exposure. The P5 and P7 primers that remain at the gold patches are capable of supporting clonal amplification of libraries (P5/P7).

Library elements are produced as follows. A genomic DNA (gDNA) library is fragmented and forked adapters having primer binding sites that are complementary to the P5 and P7 primers are ligated to the gDNA fragments, according to Illumina commercial sample preparation protocols.

Super-Poisson cluster array formation is carried out as follows. A solution is prepared containing the library elements (in double stranded form) and TWISTAMP® Basic reagent (TwistDx, Cambridge UK). The TWISTAMP® Basic reagent contains an enzyme mixture that can support template dependent amplification on the surface (DNA polymerase, single stranded binding protein and recombinase). The concentration of the library elements in solution is controlled such that the rate of hybridization capture of a library element by any feature is much lower than the rate of clonal amplification and such that there is sufficient exhaustion of the oligos available on the feature to capture another library element.

Optimal or otherwise desired concentration of the library elements for the solution can be determined empirically by titration using the above super-Poisson cluster array formation protocol followed by a sequencing run on an Illumina Sequencing device (e.g., GENOMEANALYZER®, HISEQ® or MISEQ® instruments).

EXAMPLE II

Characterization of Patterned Cluster Arrays Created Under Kinetic Exclusion Conditions

This example demonstrates super-Poisson loading of monoclonal clusters onto patterned features using kinetic exclusion conditions.

A patterned flow cell was prepared as follows. Glass flow cells (Illumina, Inc., San Diego, Calif.) were coated with gold pads using a lift-off approach as described in U.S. Pat. No. 8,778,848, which is incorporated herein by reference in its entirety. Briefly, a photoresist layer was evenly coated over the surface of the glass flow cell and patches of the photoresist were removed by photolithography to expose patches of the glass surface. A layer of gold was then deposited on the surface to form a continuous thin film over the photoresist regions and glass patches. Gold was deposited using e-beam evaporation as set forth in Thornton, Ann. Rev. Mater. Sci. 7:239-60 (1977), which is incorporated herein by reference in its entirety. The photoresist layer was then removed by acetone lift off to leave a hexagonal pattern of gold pads, wherein each of the gold pads was circular in shape, had a diameter of 500 nm, and was surrounded by interstitial regions of glass surface. The gold patterned flow cell was then coated with silane-free acrylamide (SFA) as described in WO 2008/093098 (which is incorporated herein). Primers were grafted to the polymerized SFA via a nitrobenzyl UV cleavable moiety (Glenn Research, Sterling, Va.). The flow cell was positioned on a UV (302 nm) light source such that the gold pads created a mask for primers attached over the pads while any primers attached over interstitial regions were cleaved due to UV light exposure. Cleaved primers were washed away leaving primers attached over the gold pads.

Clusters were grown on the gold pads using the TWISTAMP® Basic kit (TwistDx, Cambridge UK) as follows. A double stranded PhiX DNA library was mixed at different concentrations in the TWISTAMP® Basic Rehydration buffer and magnesium acetate reagents. The concentrations of PhiX DNA tested were about 72 pM, about 144 pM, about 432 pM and about 864 pM. These concentrations were in excess of the typical range of about 9-10 pM DNA used for standard seeding of Illumina flow cells. Also, the PhiX DNA was double stranded in contrast to standard seeding of Illumina flow cells where template DNA is in single stranded form. The PhiX DNA containing mixtures were used to rehydrate TWISTAMP® Basic freeze-dried pellets and then flushed into respective lanes of the patterned flow cell at about 38° C. Incubation was continued for about 1 hour at about 38° C. before washing with HT2 wash buffer (Illumina, Inc., San Diego Calif.) and SyBr Green staining the clusters. Clusters were then processed for sequencing by LMX1 treatment for about 30 minutes to linearize the DNA in the clusters, about 0.1N NaOH denaturation and hybridization of sequencing primer. The flow cell was then sequenced for 26 cycles on an Illumina HISEQ® 2000 instrument.

Visual inspection of flow cell images showed that clusters were spatially ordered in a pattern corresponding to the pattern of gold pads on the surface. FIG. 1(a) shows a composite image for all four color channels obtained after a first sequencing cycle using a flow cell produced by the kinetic exclusion methods set forth above. For comparison, FIG. 1(b) shows a composite image obtained after a single sequencing cycle for a standard flow cell having randomly located clusters.

Analysis of the pair distribution function (PDF) and nearest neighbor (NN) function for a composite image of the flow cell also indicated a high degree of order. Raw cluster density was calculated to be about 640,000 clusters per square millimeter for the image. The NN function was used to measure the average distance between nearest neighbor clusters in the image. As shown in FIG. 2, the NN function yielded predominantly a single peak around 2.3 pixels. This was consistent with the expected 1 micron pitch pattern for the pads, thereby suggesting a highly ordered array of clusters. Random clustering in contrast produces a much broader peak, with lower values approaching the detection limit of the cluster picking algorithm (1.2 pixels). The PDF in FIG. 2 is consistent with the expected structure for an ordered hexagonal array. For example, the PDF function showed an expected primary peak at about 2.66 pixels and higher-order peaks corresponding to neighbors beyond the nearest were clearly visible and present at the expected peak ratios. Only a slight shift in peak location between the NN and PDF functions was observed. This low level of jitter indicated that that deviation from the theoretically perfect positions was quite low and well within acceptable levels.

Visual inspection of composite four color images also revealed an absence of undesirable pad hopping. Pad hopping refers to the process of several adjacent pads being amplified from the same template sequence. Pad hopping is visually characterized in a four color image as contiguous patches of clusters that have the same color. The absence of the same color patches for flow cells produced under kinetic exclusion conditions as set forth in this example indicated that undesirable levels of pad hopping did not occur. FIG. 3 provides a more quantitative representation of cluster color and spatial position indicating that pad hopping was not a problem. Specifically, FIG. 3 shows a scatter plot of spatial positions of clusters that align to the first 5 genomic positions of PhiX genome. The different genomic positions are indicated by exes, asterisks, squares, triangles and diamonds. The 5 symbol types are randomly distributed in the figure and do not clump, which indicates that pad hopping was not a problem.

Sequence analysis for the 26 cycles of data was performed for the flow cells produced using kinetic exclusion conditions. The results indicated that about 64% of the pads were occupied and about 56% of the pads had clusters that were clonal. Thus, the methods produced a nearly 2 fold increase in clonal clusters over what is expected from Poisson loading, which would have predicted about 36% of the pads being clonal if about 64% of them were occupied. These results clearly showed super-Poisson loading.

EXAMPLE III

Active Electrical Desorption and Patterning of Biomolecules

This example demonstrates a method to spatially pattern biomolecules using electric fields. The methods described in this example rapidly seed DNA at target sites and electrochemically repel biomolecules from interstitial regions, resulting in highly patterned, addressable arrays of DNA clusters. The results shown here demonstrate the formation of flow cells having patterns of monoclonal nucleic acid clusters.

The method described in this example employs an electrical potential applied across one conductive surface and an electrolyte, or across two conductive surfaces to actively desorb either physadsorbed or chemically conjugated molecules from one or both of the electrically biased surfaces. This active desorption method does not require any surface chemistry/surface modification, can desorb molecules very quickly (less than 5 minutes) and is less sensitive to process conditions than passive desorption methods. The conductive surfaces can be metallic (e.g., titanium, indium tin oxide) or semiconducting in nature and the applied potential can be AC or DC, resulting in an electrochemical reaction at the electrode/electrolyte interface. Applying an electric field improves the signal (at the sites of interest) to noise (from the interstitial regions) by an order of magnitude. The method described in this example can also be applied to planar electrodes for selective desorption, selective refunctionalization of electrodes and electrochemical patterning of species.

Flow Cell Architecture

The two architectures described above for the electrochemical desorption of biomolecules are illustrated in FIGS. 4(a) and 4(b). Specifically, Indium Tin Oxide (ITO) was used as a conductive, transparent electrode material. ITO was deposited on a D263 surface via radio frequency sputtering. FIG. 4(a) shows the electrical potential applied across the conductive ITO layer and the electrolyte. FIG. 4(b) shows the potential applied across two parallel conductive ITO plates separated by a liquid medium. Both architectures can be used to electrically desorb species from the surface of the ITO. The gold (Au) nano-patterned sites are useful for targeted capture of thiolated biomolecules (e.g., thiolated avidin). The Au sites are separated from the underlying ITO using a dielectric spacer (e.g., SiO₂, SiN, diamond like carbon) to prevent electrochemistry on the Au.

The architecture in FIG. 4(b) can also be used to simultaneously rapidly concentrate DNA (e.g., by 100 fold) at the flow cell surface using electric fields as shown in the time lapse images of FIG. 4(c). In these experiments, a potential (V) of about 2V was applied across a gap of about 100 μm separating the two ITO surfaces. The increase in fluorescence over time, as observed using total internal reflection fluorescence (TIRF) imaging in FIG. 4(c), is due to a large increase in the surface concentration of PhiX control DNA (labeled with YOYO dye) under an applied electric field at the top surface of the flow cell. Thus, the technique outlined here can be used to simultaneously electrochemically desorb biomolecules from the interstitial region whilst facilitating rapid seeding.

Experimental Workflow

The experimental workflow for active desorption experiments is outlined in FIG. 5. The method involves coating avidin on the surface of a flow cell, followed by coating with silane free acrylamide (SFA) and grafting primers to the SFA. SFA coating and grafting of P5 and P7 primers is carried out as described in WO 2008/093098 (which is incorporated herein by reference in its entirety). However, in the present methods, avidin is electrochemically patterned on Au or dielectric sites (separated by ITO interstitial regions) that are present on the flow cell surface using an electrical desorption step prior to SFA coating. Also, following P5 and P7 primer grafting, the electric field is applied to both rapidly seed the DNA on the Au or dielectric sites and to electrochemically desorb biomolecules (DNA, avidin, primers) from the ITO interstitials. In an example, about 2V is applied to effectively desorb molecules. Field durations of as little as about 5 minutes can effectively desorb the majority of molecules in the interstitial regions. In addition, the results suggest that primer concentration in the interstitial region also decreases after electric field step. Cluster amplification is next performed as described in Bentley et al. Nature 456:53-59 (2008), followed by cluster staining using a dsDNA intercalating dye, then microscope imaging. The flow cell was then sequenced to determine cluster clonality using a HISEQ® 2000 DNA sequencer instrument (Illumina, Inc. San Diego). A schematic showing the effects of field assisted seeding and electrochemical desorption is shown in FIG. 5.

Experimental Results

FIG. 6 illustrates results achieved using the flow cell architecture from FIG. 4(b), both with electric field (FIG. 6(a)) and without electric field (FIG. 6(b)). In the presence of the electric field, clusters are highly confined to the about 2 μm Au sites with very little fluorescence observed in the interstitial areas. In the about 2 μm sites, clusters are highly polyclonal due to the large size of the Au pad. The degree of polyclonality can be decreased by decreasing pad size to inhibit multiple templates from seeding via steric exclusion or polyclonality can be deceased using kinetic exclusion conditions. Also note, pixel intensity in the interstitial regions is close to 0 (line profile of FIG. 6(a)). In contrast, clusters are present on both the Au and the interstitial ITO surfaces in the absence of the electric field. The periodic pattern observed in the line profile of FIG. 6(a) is not observed in the line profile of FIG. 6(b), confirming that the cluster confinement is the result of the electric field.

The electronic field technique can be used to spatially pattern clusters on both micron sized sites as well as nano-patterned sites over large areas. Large area images of the patterned clusters seeded on about 2 μm diameter Au sites and about 200 nm diameter Au sites are illustrated in FIGS. 7(a) and 7(b), respectively, along with their corresponding Fourier Transforms (FFT). The clusters are well defined and highly patterned with very little non-specific binding in the ITO interstitial areas. This is further confirmed by the well defined spots seen in the FFT, suggesting an ordered or patterned network. The cluster occupancy in the nano-patterned features in FIG. 7(b) is about 40-50%, but can be increased further by using higher avidin concentrations or by manipulating the voltage waveform. The same chemistry/process can be used to cluster with high spatial precision on dielectric sites as well. Ordered clusters on about 700 nm diameter SiO₂ sites are shown in FIG. 8.

Mechanism

The data suggests that the spatial patterning of clusters is facilitated in the presence of an electric field. This is likely due to the electrochemical removal of biomolecules (e.g., DNA, proteins and primers) in the interstitial regions. Grafted primer intensity is seen to decrease when the electric field is applied as seen using hybridization assays with probes labeled with Texas Red (TR). FIG. 9(a) illustrates Typhoon scans showing TR fluorescence intensity (which are quantified in FIG. 9(b)) for hybridization assays carried out in the flow cell before and after application of the electric field. Fluorescence intensity decreases by more than a factor of two after application of the electric field, confirming the removal of primers from the SFA. To increase the cluster intensity, the flow cell was re-coated with SFA and re-grafted with P5, P7 primers. This resulted in an appreciable increase in TR intensity. Thus, it is likely possible to seed DNA, electrochemically remove non-specifically bound molecules in interstitial regions, recoat SFA and re-graft primers to obtain high intensity, spatially patterned clusters.

Direct DNA Hybridization

The spatial patterning of clusters was also observed in experiments involving the direct hybridization of phiX ssDNA to the P5, P7 primer lawn. A schematic of the process is shown in FIG. 10(a). These experiments were conducted on about 2 μm Sift sites on ITO. The same process can be applied to nanopatterned sites with a variety of dielectric materials forming the sites. Neither biotinylated DNA, nor avidin are required in these experiments, thus resulting in fewer chemistry steps, whilst maintaining cluster specificity on the sites. The specificity is likely the result of electrochemical desorption of primers in the interstitial regions. FIG. 10(b) shows clusters formed on about 2 μm Sift sites in the presence of an electric field (about 2V, about 0.1 Hz) using the direct hybridization approach. Well patterned clusters are visible with very little in the interstitial regions. FIG. 10(c) is the same experiment in the absence of an electric field and shows that clusters are randomly oriented on both the SFA and the ITO interstitial regions with no distinct order present in the absence of the electric field. These results confirm that electric fields can be used to assist spatial patterning of nucleic acid cluster formation.

FIG. 11 is a flow chart of a method 100 for generating genetic clusters on a flow cell according to an example. The method 100 is performed according to the teachings described herein. At 102, a first reagent mixture is mixed with an amount of target nucleic acids to define a first solution. The first solution is also referred to herein as a target solution because the first solution includes a substantial, non-trace amount of target nucleic acids.

The target nucleic acids may be DNA from a genetic library to be sequenced. The target nucleic acids are prepared as strands with adapters at the ends that are configured to bind to corresponding primers at amplification sites of the flow cell. The first reagent mixture is composed of various reagent components including, but not limited to, NTPs and one or more replication enzymes. The one or more replication enzymes may include polymerase, recombinase, helicase, and/or the like. The reagent mixture may include additional reagent components besides the NTPs and the one or more replication enzymes, such as primers, single stranded binding proteins, buffers for fluidic transport (e.g., water, a surfactant, etc.), a crowding agent, magnesium, and/or the like. In one example, the first reagent mixture is mixed with the target nucleic acids in a mixing or cache reservoir on a reagent manifold that is fluidly connected to a flow cell. The target nucleic acids are free-floating within the target solution.

At 104, the target solution is flowed over an array of amplification sites on a flow cell to produce clonal populations of amplicons on the flow cell. Flowing the target solution over the amplification sites produces the clonal populations of amplicons at the amplification sites according to the kinetic exclusion amplification conditions described herein. The clonal populations of amplicons are also referred to herein as clonal clusters and genetic clusters. In an example, the target solution is flowed from the mixing reservoir of the reagent manifold to the flow cell and through an inlet port of the flow cell to contact the array of amplification sites.

The amplification sites may be located at structural features along a surface of the flow cell. The structural features are concave wells along the surface in one example, but may be other features such as beads in other examples. The wells are separated from each other by interstitial regions of the surface of the flow cell. In an example, prior to flowing the target solution over the amplification sites, the flow cell is prepared by attaching P5 and P7 primers to the surface of the flow cell at the amplification sites. In one example, the primers may be attached to the flow cell via coating the patterned flow cell with silane-free acrylamide (SFA) and then grafting the primers to the polymerized SFA via a nitrobenzyl UV cleavable moiety. Primers optionally may be guided to the amplification sites and away from the interstitial regions by e-field assisted transport. Alternatively, the primers may be grafted to both the wells and the interstitial regions, but the primers at the interstitial regions are removed due to UV light exposure, polishing, or another process that removes the primers from the interstitial regions without removing the primers located within the wells. The prepared flow cell includes a lawn of primers at each of the amplification sites (e.g., within each of the wells) and has only a small amount of primers, if any, within the interstitial regions.

The target solution may be actively flowed over the amplification sites using one or more pumps that require an energy source to propel the target solution relative to the flow cell. In another example, the target solution may passively flow over the amplification sites by opening one or more valves and allowing gravity and/or diffusion to move the target solution over the amplification sites. The target nucleic acids are free-floating within the target solution as the target solution is flowed over the amplification sites. The number of target nucleic acids in the target solution exceeds the number of amplification sites, such as wells, on the flow cell.

At 106, the target solution is incubated on the flow cell. The target solution is incubated by being retained in contact with the array of amplification sites on the flow cell for a designated time period at designated conditions (e.g., temperature, pressure, humidity, etc.). For example, the target solution may be incubated on the flow cell at a temperature between about 20 degrees Celsius and about 50 degrees Celsius, such as between about 30 and about 42 degrees Celsius, for a time between about 30 minutes and about 90 minutes, such as about 40 minutes or about 60 minutes. The incubation conditions may be different in alternative examples.

During incubation, the target solution reacts on the flow cell to produce clonal populations of amplicons at the amplification sites. The clonal populations of amplicons originate from corresponding target nucleic acids. For example, the target nucleic acids bind to the primers attached to the amplification sites via hybridization between the adapter ends and the primers to attach the target nucleic acids to the flow cell. The target nucleic acids are transported to the amplification sites and bind to the primers at a transport rate. The transport rate describes the rate of seeding of a target nucleic acid at an amplification site, such as a well. The transport rate may depend on the concentration of target nucleic acids in the target solution that is flowed over the amplification sites. For example, a greater concentration of the target nucleic acids in the target solution may increase the transport rate compared to the transport rate resulting from a lower concentration of the target nucleic acids in the target solution. The transport rate can be controlled by controlling the concentration of the target nucleic acids in the target solution. The transport rate can also be controlled by controlling the viscosity of the target solution, controlling an average size of the target nucleic acids, and/or deciding whether to add a molecular crowding reagent in the target solution. For example, the transport rate can be reduced by increasing the viscosity of the target solution, increasing the average size or length of the strands of the target nucleic acids, and/or adding a molecular crowding reagent (which obstructs the ability of the free-floating nucleic acids to move to and bind to the primers at the amplification sites). The transport rate can be increased by reducing the viscosity of the target solution, reducing the average size of the target nucleic acids, and/or not using a molecular crowding reagent.

The presence of the reagent mixture in the target solution allows simultaneous transport of the target nucleic acids to the amplification sites and amplification of the target nucleic acids that are already bound to the amplification sites. For example, the enzymes use the nucleotides of the NTPs to produce the amplicons, which are copies of the target nucleic acids. The amplicons are bound to the amplification sites. The amplicons are produced at an amplification rate, which can be controlled based on the concentrations of the reagent components within the first reagent mixture, such as the concentrations of the NTPs and the one or more replication enzymes. For example, greater concentrations of polymerase and recombinase may increase the amplification rate relative to the amplification rate resulting from lower concentrations of polymerase and recombinase. The amplification rate may also be affected by controlling the temperature at the amplification sites and/or controlling properties of the primers at the amplification sites. For example, the sequence, length, and/or type of the primers can be modified or selected to affect the amplification rate.

The amplification rate is controlled to exceed the transport rate in order to provide kinetic exclusion amplification. For example, the amplification rate may significantly exceed the transport rate such that once a first target nucleic acid binds to one primer at an amplification site, many amplicons originating from the first target nucleic acid are formed on other primers at the amplification site before other target nucleic acids are able to bind to the primers at the same amplification site. The result is a clonal population (or cluster) of amplicons at the amplification site originating from the first target nucleic acid. The different amplification sites have clonal populations of amplicons that originate from different target nucleic acids, such that the clonal population of amplicons at a second amplification site originates from a second target nucleic acid that differs from the first target nucleic acid. Therefore, one well along the flow cell may be filled with amplicons originating from a first target nucleic acid, and a second well may be filled with amplicons originating from a second target nucleic acid in the target solution. The amplification rate exceeds the transport rate by a predetermined amount or extent such that the subsequent target nucleic acids that arrive at a particular amplification site after a first target nucleic acid arrives at the site are kinetically excluded from seeding to that particular site.

The spatially-separated clonal clusters of amplicons are used for genetic sequencing. For example, the strands of amplicons may be used as templates in the sequencing-by-synthesis procedure that receive fluorescently-labeled nucleotides. The fluorescently-labeled nucleotides emit a characteristic signal upon excitation, which is used to determine the sequence of the target nucleic acids.

At 108, the target solution is removed from the flow cell. For example, the target solution is removed from the flow cell such that there are no free-floating target nucleic acids present along the surface of the flow cell that are not bound to the surface. Therefore, target nucleic acids within the target solution that do not hybridize to one of the primers on the surface of the flow cell are washed away from the flow cell. The target solution may be removed by pumping the target solution from the flow cell, flushing the flow cell with a neutral solution to wash the target solution from the flow cell, draining the target solution from the flow cell using gravity, and/or the like. The clonal clusters of amplicons and the target nucleic acids bound to the flow cell at the amplification sites remain on the flow cell after the target solution is removed.

In an example, a secondary exclusion amplification step is performed subsequent to the initial exclusion amplification step in order to increase the number of amplicons in the clonal clusters at the amplification sites on the flow cell. An increased number of amplicons in the clusters at the amplification sites provide more signals and a better signal-to-noise ratio during sequencing-by-synthesis than clusters with fewer amplicons. For example, the signal intensity may increase due to a greater number of amplicons in the clusters, while the background noise remains constant, resulting in a better signal-to-noise ratio. The better signal-to-noise ratio allows for more accurate and efficient sequencing because there is less likelihood of errors at the base level.

At 110, a second reagent mixture is mixed to define a second, target-less solution that lacks additional target nucleic acids. In one example, the target-less solution is void of target nucleic acids. For example, the second reagent mixture may be mixed in a second mixing reservoir that is different than the mixing reservoir used to mix the first reagent mixture with the target nucleic acids to define the target solution. Although this mixing step 110 is illustrated in the method 100 after the target solution is removed from the flow cell, optionally the second reagent mixture may be mixed before the target solution is removed from the flow cell, such as concurrently with the mixing of the first reagent mixture and the target nucleic acids to define the target solution, when the target solution is incubating on the flow cell, or the like. The target-less solution, in one example, is a fresh solution that does not include any recycled portion of the target solution that already flowed over the amplification sites.

In an alternative example, the target-less solution may include a non-zero, trace amount of target nucleic acids. For example, when the first, target solution is flowed from the mixing reservoir to the flow cell, a residual amount of the target solution may be retained within the mixing reservoir without flowing to the flow cell. Furthermore, the second reagent mixture may be subsequently mixed within the same mixing reservoir, such that the residual amount of the target solution mixes with the second reagent mixture to define the target-less solution. The resulting target-less solution may contain a trace amount of the target nucleic acids from the residual amount of the target solution in the mixing reservoir. The concentration of the target nucleic acids in the target-less solution is less than 100 ppm, which may be sufficiently low to have a negligible effect on the reaction of the target-less solution on the amplification sites to produce additional amplicons.

The second reagent mixture in the target-less solution may include the same or different types of reagent components as the first reagent mixture in the target solution. For example, the second reagent mixture may include the same types of NTPs and the same types of replication enzymes as the first reagent mixture. It is noted that although at least some of the same types of reagent components may be used for both solutions, the second reagent mixture is composed of fresh amounts of the reagent components. For example, no portion of the first, target solution, after flowing through the flow cell, is recycled into the mixing reservoir to define the target-less solution.

The reagent components in the second reagent mixture may include one or more of NTPs, polymerase, recombinase, helicase, single stranded binding protein, crowding agents, buffers, and/or the like. The second reagent mixture may include different amounts and/or concentrations of the reagent components relative to the first reagent mixture in the target solution. For example, the second reagent mixture may include a greater concentration of replication enzymes, such as polymerase, recombinase, and/or helicase, relative to the first reagent mixture in order to increase the replication rate at which the amplicons are formed at the amplification sites. In another example, the second reagent mixture may include a greater quantity of a buffer component (e.g., water, a surfactant, or a water-surfactant mixture) relative to the first reagent mixture to compensate for the lack of adding the target nucleic acids to the second reagent mixture. The second reagent mixture optionally may include one or more different types of reagent components than the first reagent mixture, such as different proteins, primers, or the like. For example, the second reagent mixture may include primers that are not present in the first reagent mixture. The primers may be P5 primers having a P5 primer sequence and/or P7 primers having a P7 primer sequence.

At 112, the target-less solution is flowed over the array of amplification sites on the flow cell. The target-less solution may be pumped or drained from the respective reservoir containing the target-less solution to the flow cell. As described above, the target-less solution may be completely void of target nucleic acids or, alternatively, may include only a trace amount of target nucleic acids due to retention of a residual amount of the target-solution in the mixing reservoir used to prepare the target-less solution. Since the target-less solution does not include more than a trace amount of target nucleic acids, the flowing of the target-less solution over the amplification sites does not cause an appreciable amount of additional seeding of target nucleic acids to the amplification sites. More specifically, no additional target nucleic acids bind to primers at the amplification sites. The target nucleic acids of the genetic library bind to the primers at the amplification sites generally only when flowing the target solution through the flow cell.

At 114, the target-less solution is incubated on the flow cell. The target-less solution may be retained in contact with the array of amplification sites on the flow cell for a designated time period at certain designated conditions (e.g., temperature, humidity, pressure, etc.). The time period and/or conditions may be similar or identical to the incubation of the target solution. In one example, the target-less solution may be incubated on the flow cell at a temperature of about 38 degrees Celsius for between about 20 and about 60 minutes, although the incubation conditions may be different in other examples.

The incubation of the target-less solution on the flow cell increases the number of amplicons in the clonal populations or clusters at the amplification sites, providing more complete clustering amplification. For example, during the initial exclusion amplification reaction, the target nucleic acids and the produced amplicons may bind to some, but not all, of the primers at each amplification site. Therefore, there may be a number of the primers at the amplification sites that are not bound to either a target nucleic acid or an amplicon and are exposed for binding. Such primers define an exposed subset of primers at each amplification site. The reagent mixture in the target-less solution produces additional amplicons on the exposed primers, reducing the number of primers in the exposed subset. For example, the second reagent mixture reacts with the existing amplicons in the clonal cluster to produce new amplicons that bind to the exposed primers.

Instead of, or in addition to, producing amplicons on pre-existing exposed primers at the amplification sites, the second reagent mixture may include additional primers. In one example, the second reagent mixture includes a primer, such as a P5 primer. Prior to flowing the target-less solution over the flow cell, the existing P5 primers (including the P5 strands of the amplicons in the clusters) at the amplification sites are linearized and removed, leaving mainly the P7 strands of the amplicons in the clusters and any leftover, exposed (e.g., unused) surface-bound P7 primers. Since the target-less solution includes P5 primers from the second reagent mixture therein, flowing the target-less solution over the flow cell promotes further amplification of the clusters onto the exposed surface-bound P7 primers. Some of the surface P7 primers were exposed after the initial exclusion amplification because the DNA cluster strands need to bridge over and remain bound to the surface at both ends. Steric hindrance may restrict access to all of the available exposed surface primers. By removing one of the primers (e.g., the P5 primer) from the surface after the initial exclusion amplification step using the first, target solution, the accessibility to the other primer (e.g., the P7 primer) remaining on the surface is increased. Furthermore, one end of the amplicon cluster strand is freed from needing to be surface-bound for amplification.

In another example, secondary amplification may be accomplished with the second reagent mixture containing no extra primers. For example, the surface bound P5 primers may be linearized and removed from the amplification sites prior to flowing the target-less solution, without denaturing the amplicon clusters such that the P5 strands of the clusters remain surface-bound. The target-less solution flowed over the amplification sites in this state may produce more copies of the P5 strands via strand invasion using the unused P7 primers in a linear amplification manner. The secondary amplification in this example is enabled by making the unused P7 primers more accessible via linearization of one end of the clusters.

Optionally, the second reagent mixture includes primers that attach to the surface of the flow cell akin to a second grafting step, especially in stable conditions suitable for grafting. For example, BCN (bicylononyne)-linked P5/P7 can graft to PAZAM in water or low salt buffer conditions. This second grafting step may be performed after flowing the first, target solution and before flowing the second, target-less solution. Alternatively, the primers in this second grafting step may be mixed into the second reagent mixture, as long as the grafting is compatible with the second reagent mixture. The primers in the target-less solution increase the total number of primers at the amplification sites and provide new locations at which additional amplicons may be formed to increase the number of amplicons in the clusters.

Since no additional target nucleic acids are used to form the target-less solution, the number of amplicons in the clusters can be increased without requiring additional genetic material, which may be relatively difficult and/or costly to obtain relative to the reagent components.

At 116, the second, target-less solution is removed from the flow cell prior to performing the subsequent sequencing steps with the flow cell for genetic library sequencing. For example, the target-less solution may be pumped from the flow cell, flushed from the flow cell using a neutral solution, or drained from the flow cell.

Optionally, the target solution and target-less solutions are both flowed over the amplification sites at isothermal conditions such that neither of the solutions nor the flow cell is actively heated. Furthermore, the clonal clusters are formed without the use of chemical denaturants to denature the target nucleic acids and the amplicons on the flow cell. Therefore, the method 100 may increase the yield and/or quality of nucleotide strands in the clonal clusters on the flow cell without requiring heat applications or chemical denaturants, unlike some other amplification techniques such as bridge amplification, RCA techniques, and MDA techniques.

In an alternative example of the method 100 for generating clonal clusters, the first, target solution is not removed from the flow cell prior to introducing the second, target-less solution to the flow cell. Therefore, the method 100 may skip the step 108 directed to removing the target solution from the flow cell. Instead, after incubating the target solution on the flow cell for a first time period at step 106, the target-less solution is flowed over the array of amplification sites on the flow cell at 112 while the target solution is still present on the flow cell. For example, the target solution may be incubated on the flow cell for about 20 minutes, about 40 minutes, about 60 minutes, or the like, prior to introducing the target-less solution to the flow cell. Once the target-less solution is flowed over the array of amplification sites at 112, the target-less solution mixes with the target solution on the flow cell. The second reagent mixture within the target-less solution increases the total concentration of reagents within the flow cell, which may increase the amplification rate at which the amplicons are produced. At 114, the target-less solution is incubated on the flow cell for a second time period with the target solution present. Therefore, the target solution is incubated on the flow cell for a total amount of time that is the sum of the first time period at 106 and the second time period at 114. At 116, the combined solution composed of both the first, target solution and the second, target-less solution is removed from the flow cell, such as by pumping, flushing with a neutral solution, draining, or the like, prior to performing subsequent sequencing steps with the flow cell.

FIG. 12 is a bar graph 200 showing, in one example, the signal intensity of genetic clusters on a flow cell for different approaches of cluster generation. The graph 200 illustrates how the signal intensity may compare among the different cluster generation approaches when the approaches are performed under similar environmental conditions. The graph 200 compares the approaches in relative terms and does not represent actual test results. The y-axis 202 represents the detected signal intensity of the clusters during sequencing-by-synthesis when the clusters having fluorescently-labeled nucleotides are excited, and is labeled 200-550. Three different cluster generation methods are compared and represented by corresponding bars on the graph 200. The bar 204 represents kinetic exclusion amplification (ExAmp) without any additional amplification steps performed to increase the number of amplicons in the clusters. The bar 206 represents kinetic exclusion amplification followed by conventional bridge amplification. The bar 208 represents kinetic exclusion amplification according to the examples described herein in which a first round of kinetic exclusion amplification is followed by a secondary round of kinetic exclusion amplification using a target-less solution that lacks target nucleic acids.

As shown in FIG. 12, the exclusion amplification followed by the secondary round of exclusion amplification (e.g., bar 208) has the greatest intensity, followed by the bridge amplification (e.g., bar 206) and the exclusion amplification without secondary amplification (e.g., bar 204), which has the lowest intensity. For example, if the single round of kinetic exclusion amplification at 204 produces genetic clusters with a signal intensity of about 285, then the kinetic exclusion amplification followed by bridge amplification at 206 produces genetic clusters with a signal intensity of about 320, and the kinetic exclusion amplification followed by a second round of exclusion amplification at 208 produces genetic clusters with a signal intensity of about 420. The greater signal intensity indicates that the exclusion amplification followed by the secondary round of exclusion amplification is able to provide a better signal-to-noise ratio than the other two methods. The better signal-to-noise ratio may increase the accuracy and/or efficiency of the sequencing and analysis of the genetic library relative to the other two methods.

FIG. 13 is a bar graph 300 showing, in one example, percent passing filter (% PF) values for the same cluster generation methods as the bar graph 200. The graph 300 illustrates how the % PF values attributable to the different cluster generation approaches may compare when the approaches are performed under similar environmental conditions. The graph 300 compares the approaches in relative terms and does not represent actual test results. The y-axis 302 represents a percentage of the clusters generated by each of the three methods that exceed a designated chastity filter condition, indicating that those clusters have sufficient quality to be used for sequencing, and is labeled from 60%-78%. The bar 304 represents the kinetic exclusion amplification without a secondary amplification step, the bar 306 represents the kinetic exclusion amplification followed by bridge amplification, and the bar 308 represents the kinetic exclusion amplification followed by the secondary round of kinetic exclusion amplification. As shown in FIG. 13, if the single round of kinetic exclusion amplification at 304 produces genetic clusters with about 65% of the clusters passing filter, then the kinetic exclusion amplification followed by bridge amplification at 306 produces genetic clusters with about 71% of the clusters passing filter, and the kinetic exclusion amplification followed by a second round of exclusion amplification at 208 produces genetic clusters with about 73% of the clusters passing filter. Therefore, the exclusion amplification followed by the secondary round of exclusion amplification using a target-free solution can provide the greatest yield of quality clusters relative to the other clustering approaches under similar environmental conditions.

FIG. 14 is a schematic illustration of a fluidic system 400 for generating clonal clusters according to an example. The fluidic system 400 may be used to perform the method 100. The fluidic system 400 may be similar to the fluidic systems set forth in U.S. Pat. No. 9,410,977, which is incorporated by reference herein in its entirety. The fluidic system 400 in the illustrated example includes a patterned flow cell 402, a reagent manifold 404, a reagent tray or cartridge 406, a controller 408, and a pump 410. Alternatively, the fluidic system 400 may include additional components, fewer components, and/or at least one different component than the illustrated example.

The flow cell 402 includes multiple lanes 412 that extend between and are fluidly connected to an inlet port 414 and an outlet port 416 of the flow cell 402. The lanes 412 may include wells or other features on the surfaces thereof to define the amplification sites on which the clonal populations or clusters of amplicons on produced. The reagent manifold 404 includes a valve 418 that is in fluid communication (e.g., fluidly connected) with the inlet port 414 of the flow cell 402. The valve 418 may include or be connected to at least one mixing reservoir (also referred to herein as cache reservoirs), which is not shown in FIG. 14. The reagent manifold 404 further includes a plurality of channels 420 and ports 422. The channels 420 extend between and fluidly connect the ports 422 to the valve 418 (and any mixing reservoirs associated with the valve 418). The reagent manifold 404 may have multiple valves 418 in other examples. Although not shown, the reagent manifold 404 may include sippers that are disposed in the corresponding ports 422.

The reagent tray 406 includes multiple reagent reservoirs (not shown) that contain different reagents. The reagent manifold 404 is mounted over the reagent tray 406 to align the sippers with the reagent reservoirs such that the sippers enter the corresponding reagent reservoirs and contact the reagents therein. The sippers extract the reagents from the reagent reservoirs of the tray 406 to supply the reagents to the flow cell 402 through the channels 420 and the valve 418.

The controller 408 includes one or more processors (not shown) or other logic-based devices that perform operations based on instructions stored on a tangible and non-transitory computer readable storage medium or memory (not shown). The controller 408 may additionally or alternatively include one or more hard-wired devices that perform operations based on hard-wired logic of the devices. The controller 408 may represent the hardware that operates based on software or hardwired instructions, the software that directs hardware to perform the operations, or a combination thereof. The controller 408 is communicatively coupled (e.g., via one or more wired or wireless connections) to the pump 410 and the valve 418. For example, the controller 408 is able to control the operations of the pump 410 and the valve 418 by communicating control signals along the wired or wireless connections to the respective devices. The controller 408 may control the valve 418 by controlling which of the channels 420 are permitted to have fluid in the channel 420 flow through the valve 418 to the flow cell 402. The controller 408 controls the pump 410 by controlling pressure differentials created by the pump 410 to propel fluid along the fluidic system 400. The pump 410 in the illustrated example is operatively coupled to the flow cell 402, but the pump 410 alternatively may be connected to the reagent manifold 404.

In an example, the controller 408 controls the pump 410 and the valve 418 to mix and flow the first, target solution through the inlet port 414 over the array of amplification sites on the flow cell 402. The target solution includes the target nucleic acids and the first reagent mixture. The target nucleic acids may be combined with the first reagent mixture within the reagent manifold 404, such as within one of the mixing reservoirs (not shown) associated with the valve 418. For example, a first channel 420A of the channels 420 may contain a genetic sample template that includes the target nucleic acids in a buffer, such as water or another solvent. The sample template may be extracted from the reagent tray 406 by a sipper, or alternatively may flow into the channel 420A from another source other than the tray 406. A second channel 420B of the channels 420 may contain one or more reagent components of the first reagent mixture, such as NTPs, polymerase, single stranded binding protein, and one or more buffers (e.g., water, surfactants, or the like). A third channel 420C and a fourth channel 420D may contain other reagent components of the first reagent mixture, such as recombinase within the third channel 420C and magnesium and a crowding agent within the fourth channel 420D. Although not specifically mentioned, all of the reagent components may be dissolved in a solvent, such as water or another buffer. Keeping some of the reagent components separated until the target solution is ready to be used may increase the usable lifespan of the reagent mixture, as some of the reagent components may be unstable when mixed with other reagent components.

In one example, the controller 408 controls the pump 410 and the valve 418 to mix certain designated quantities of the sample template with the reagent components within the different channels 420A-D to define the target solution within the manifold 404 prior to flowing the target solution through the inlet port 414 of the flow cell 402. For example, the components of the target solution may be mixed within one of the mixing reservoirs. Alternatively, the components of the target solution may be separated until the components are allowed to mix within an inlet conduit (e.g., tube, pipe, or channel) 424 that connects the valve 418 to the inlet port 414 or within the flow cell 402.

As described above, the target solution reacts on the flow cell 402 to produce clonal populations of amplicons at the amplification sites originating from the corresponding target nucleic acids. During the exclusion amplification process, the target nucleic acids are transported to the amplification sites simultaneously with the amplification of the target nucleic acids already bound to the amplification sites to produce the amplicons. The controller 408 may manipulate the pump 410 and/or the valve 418 to control the concentration of the target nucleic acids and the concentration of the first reagent mixture in the target solution in order for amplification rate to exceed the transport rate. For example, the controller 408 may reduce the concentration of the sample template and/or increase the concentration of one or more components of the first reagent mixture in order to maintain the amplification rate at a significantly greater rate than the transport rate for kinetic exclusion.

The controller 408 may also be configured to control the incubation conditions of the target solution on the flow cell 402, such as the temperature, pressure, humidity, and the like, within the flow cell 402. After a designated amount of incubation time, the controller 408 may control the pump 410 to remove the target solution from the flow cell 402. The target solution may flow through the outlet port 416 into a waste reservoir 426. Optionally, a portion of the target solution may be recirculated through a conduit 428 to the reagent manifold 404 and/or the tray 406 to be used for refresh pumping or the like. The target solution is removed from the flow cell 402 such that no free-floating target nucleic acids are present in the flow cell 402 after removing the target solution. For example, all of the target nucleic acids present at the amplification sites after removal of the target solution are bound to primers within the clonal clusters.

In an example, after flowing the target solution through the flow cell 402, the controller 408 controls the pump 410 and/or the valve 418 to mix and flow the target-less solution through the inlet port 414 over the array of amplification sites on the flow cell 402. The target-less solution includes the second reagent mixture and lacks (e.g., is void of) additional target nucleic acids. For example, the controller 408 may control the mixing of the reagent components within the second, third, and fourth channels 420B-D within a mixing reservoir (not shown) on the manifold 404 to define the target-less solution. The controller 408 controls the valve 418 to prevent the sample template within the first channel 420A from being added to the mixing reservoir, such that the resulting target-less solution does not include additional target nucleic acids. In one example, the second reagent mixture is mixed within a different mixing reservoir than the mixing reservoir used to mix the first reagent mixture with the sample template to define the target solution. In an alternative example, the second reagent mixture is mixed within the same mixing reservoir that previously contained the target solution, such that a residual amount of the target solution (including a trace amount of target nucleic acids) may be present within the target-less solution. Therefore, the second, target-less solution is either void of target nucleic acids or includes a trace amount of target nucleic acids that does not cause additional seeding at the amplification sites of the flow cell 402.

The second reagent mixture may differ from the first reagent mixture in the types, amounts, and/or concentrations of the reagent components. For example, the first reagent mixture and the second reagent mixture may both include a buffer component, such as water, a surfactant, or a water-surfactant solution. Since the target-less solution lacks the sample template, the controller 408 optionally may include a greater quantity of the buffer component within the target-less solution relative to the amount of the same buffer component within the first reagent mixture. The additional amount of buffer compensates for the reduced volume caused by the lack of the sample template. As a result of the increased volume of buffer, the volume of the target-less solution may be similar or identical to the volume of the target solution. Furthermore, controlling the amount of buffer also affects the concentrations of the reagent components in the second reagent mixture, such that the concentrations may be controlled to be similar or identical to the concentrations of the reagent components within the target solution. Optionally, the controller 408 may vary at least some of the types (e.g., different enzymes, proteins, oligos, or the like), amounts, and/or concentrations of the reagent components of the second reagent mixture relative to the first reagent mixture, such as to modify the amplification rate.

The controller 408 controls the pump 410 and/or the valve 418 to flow the target-less solution to the flow cell 402. The target-less solution is incubated on the flow cell 402, where the solution reacts with the amplicons at the amplification sites in the flow cell 402 to produce additional amplicons in the clonal clusters. As described above, the secondary round of exclusion amplification using the target-less solution results in a greater yield of passing-quality clusters relative to not flowing the target-less solution through the follow cell 402. The increased yield of quality clusters may increase sequencing accuracy and/or efficiency because there are additional nucleotide strands in the clusters to produce fluorescent signals during sequencing-by-synthesis. The secondary round of exclusion amplification is also achieved without using an additional amount of a sample template that includes target nucleic acids.

Additional Notes

Throughout this application various publications, patents and patent applications have been referenced. The disclosures of these publications in their entireties are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this inventive subject matter pertains.

The terms “comprise,” “include,” “contain,” etc., and variations thereof, that are used in the specification and claims herein are intended to be open-ended, including not only the recited elements, but further encompassing any additional elements. Reference throughout the specification to “one example”, “another example”, “an example”, and so forth, means that a particular element (e.g., feature, structure, and/or characteristic) described in connection with the example is included in at least one example described herein, and may or may not be present in other examples. In addition, it is to be understood that the described elements for any example may be combined in any suitable manner in the various examples unless the context clearly dictates otherwise.

It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein. It should also be appreciated that terminology explicitly employed herein that also may appear in any disclosure incorporated by reference should be accorded a meaning most consistent with the particular concepts disclosed herein.

It is to be understood that the ranges provided herein include the stated range and any value or sub-range within the stated range. For example, a range from between about 20 degrees Celsius and about 50 degrees Celsius, should be interpreted to include not only the explicitly recited limits of from between about 20 degrees Celsius and about 50 degrees Celsius, but also to include individual values, such as about 28 degrees Celsius, about 35 degrees Celsius, about 46.5 degrees Celsius, etc., and sub-ranges, such as from about 25 degrees Celsius to about 49 degrees Celsius, from about 30 degrees Celsius to about 40 degrees Celsius, etc. Furthermore, when “about” and/or “substantially” are/is utilized to describe a value, they are meant to encompass minor variations (up to +/−10%) from the stated value.

While several examples have been described in detail, it is to be understood that the disclosed examples may be modified. Therefore, the foregoing description is to be considered non-limiting. Although the inventive subject matter has been described with reference to the examples provided above, it should be understood that various modifications can be made to the examples without departing from the scope of the inventive subject matter. Accordingly, the scope of the inventive subject matter is limited only by the claims. 

What is claimed is:
 1. A method, comprising: reacting a first solution and a different, second solution on a flow cell by flowing the first solution over an array of amplification sites on the flow cell and subsequently flowing the second solution over the array of amplification sites; the first solution including a number of target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates (NTPs) and one or more replication enzymes, the target nucleic acids in the first solution transporting to and binding to the amplification sites at a transport rate, the first reagent mixture amplifying the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids, the amplicons produced at an amplification rate that exceeds the transport rate; and the second solution including a second reagent mixture and lacking the target nucleic acids, the second solution to increase a number of the amplicons in the clonal populations at the amplification sites.
 2. The method of claim 1, wherein the second reagent mixture includes the NTPs and the one or more replication enzymes of the first reagent mixture.
 3. The method of claim 1, wherein the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein the first solution reacts on the flow cell to bind the target nucleic acids and the amplicons to a first subset of the primers, and wherein the second solution reacts on the flow cell to produce additional amplicons and bind the additional amplicons to at least some of the primers in an exposed subset of the primers different than the first subset.
 4. The method of claim 1, further comprising removing the first solution from the flow cell prior to flowing the second solution over the array of amplification sites on the flow cell such that the only target nucleic acids on the flow cell as the second solution flows over the array of amplification sites are bound to the flow cell and not free-floating within the first solution.
 5. The method of claim 1, wherein the array of amplification sites are disposed along a surface of the flow cell, wherein the first solution is flowed through an inlet port of the flow cell across the surface of the flow cell, and wherein the second solution is subsequently flowed through the inlet port across the surface of the flow cell.
 6. The method of claim 1, wherein the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein at least some of the primers bind to the target nucleic acids in the first solution responsive to flowing the first solution over the array of amplification sites, and wherein subsequently flowing the second solution that lacks the target nucleic acids over the array of amplification sites results in no additional binding of the primers to the target nucleic acids.
 7. The method of claim 1, wherein the target nucleic acids are only flowed over the array of amplification sites on the flow cell with the first solution.
 8. The method of claim 1, wherein the second reagent mixture includes the NTPs and a polymerase.
 9. The method of claim 1, wherein the second reagent mixture includes one or more of a helicase and a recombinase.
 10. The method of claim 1, wherein the second reagent mixture includes a primer having at least one of a P5 primer sequence or a P7 primer sequence.
 11. The method of claim 1, wherein the amplification sites are wells along a surface of the flow cell, the wells separated from each other by interstitial regions along the surface.
 12. The method of claim 1, further comprising controlling the transport rate of the target nucleic acids to the amplification sites using one or more of: controlling a concentration of the target nucleic acids in the first solution, controlling a viscosity of the first solution, controlling an average size of the target nucleic acids, and controlling a presence or absence of a molecular crowding reagent in the first solution.
 13. The method of claim 1, further comprising controlling the amplification rate of the target nucleic acids using one or more of: controlling a concentration of the NTPs in the first reagent mixture, controlling a concentration of the one or more replication enzymes in the first reagent mixture, and controlling the temperature at the amplification sites.
 14. The method of claim 1, wherein the first solution and the second solution are isothermally flowed over the array of amplification sites.
 15. A method, comprising: mixing a first reagent mixture with an amount of target nucleic acids within a reservoir to define a first solution, the first reagent mixture comprising nucleoside triphosphates (NTPs) and one or more replication enzymes; flowing the first solution from the reservoir over an array of amplification sites on a flow cell, the target nucleic acids in the first solution transporting to and binding to the amplification sites at a transport rate, the first reagent mixture amplifying the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids, the amplicons produced at an amplification rate that exceeds the transport rate; subsequent to flowing the first solution from the reservoir, mixing a second reagent mixture within the reservoir without adding an additional amount of the target nucleic acids to the reservoir to define a second solution, the second reagent mixture comprising fresh quantities of the NTPs and the one or more replication enzymes; and flowing the second solution from the reservoir over the array of amplification sites on the flow cell, the second reagent mixture reacting with the amplicons to increase a number of the amplicons in the clonal populations at the amplification sites.
 16. The method of claim 15, wherein the first reagent mixture and the second reagent mixture both include a buffer component, the second reagent mixture including a greater quantity of the buffer component relative to the first reagent mixture to compensate for the lack of adding the additional amount of the target nucleic acids within the second solution. 